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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/chromhmm">Debian Med / chromhmm</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/53d4d077a8b1b3ef1976ee68603251e6c241194b">53d4d077</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:35:42+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd371febdf5c385e3d51c83ff7a2ec0dfcde1f12">bd371feb</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:35:44+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.23+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/ac34772f813f01e640b2a91c2fd727c132258d12">ac34772f</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:36:13+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.23+dfsg'

Update to upstream version '1.23+dfsg'

with Debian dir 4e9297e9a9e5e88ce7fb5e8e910c59ad4949f98a</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/7775454a32572880dfbfb2778c7e9066deb62cdc">7775454a</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:36:14+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/196ec1cacb9c44e0937f4b0117f5e8b40548c543">196ec1ca</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:36:39+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).

Changes-By: lintian-brush

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/48f250d34bb651f4bee1dde863e84925132b42b1">48f250d3</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-07T17:36:40+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

debian/upstream/metadata

</a>

</li>

<li class="file-stats">

<a href="#b878cde2a28128a1ce4a4106b42d1e16efb65f66">

edu/mit/compbio/ChromHMM/BrowserOutput.java

</a>

</li>

<li class="file-stats">

<a href="#e1a765a5b2b828119bc810319c6fa07e7300eecf">

edu/mit/compbio/ChromHMM/ChromHMM.java

</a>

</li>

<li class="file-stats">

<a href="#c4dd7be4883f31af6f5731277ba2f3147cd4b40a">

edu/mit/compbio/ChromHMM/ConvertGeneTable.java

</a>

</li>

<li class="file-stats">

<a href="#6cf51526a9e3e36b9a53742e82b9e0ea219c57fc">

edu/mit/compbio/ChromHMM/NestedEliminateInitialize.java

</a>

</li>

<li class="file-stats">

<a href="#7e91b8c750d2f1f3056fc7dcbd7d4d639572d170">

edu/mit/compbio/ChromHMM/Preprocessing.java

</a>

</li>

<li class="file-stats">

<a href="#4fb31ca7c49b2c49cfd549091ba94777db11f494">

edu/mit/compbio/ChromHMM/StateAnalysis.java

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See <span class="idiff left right">http://compbio.mit.edu/ChromHMM/ or </span>https://ernstlab.biolchem.ucla.edu/ChromHMM/ for more information on ChromHMM.</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See https://ernstlab.biolchem.ucla.edu/ChromHMM/ for more information on ChromHMM.</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chromhmm (1.23+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.6.0 (routine-update)</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Remove obsolete fields Contact, Name from debian/upstream/metadata (already</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">    present in machine-readable debian/copyright).</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  Tue, 07 Sep 2021 17:36:40 +0530</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

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1

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">chromhmm (1.22+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

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2

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

</td>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               libbatik-java,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               libjheatchart-java</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Build-Depends-Indep: default-jdk</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/chromhmm</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/chromhmm.git</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: http://compbio.mit.edu/ChromHMM/</span>

</pre>

</td>

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<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,6 @@ Bug-Submit: https://github.com/jernst98/ChromHMM/issues/new</td>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Changelog: https://github.com/jernst98/ChromHMM/tags</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Repository: https://github.com/jernst98/ChromHMM.git</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Repository-Browse: https://github.com/jernst98/ChromHMM</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Contact: Jason Ernst <jason.ernst at ucla.edu></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Name: ChromHMM</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Reference:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  - Author: Jason Ernst and Manolis Kellis</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">    Title: ></span>

</pre>

</td>

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<br>

</li>

<li id="b878cde2a28128a1ce4a4106b42d1e16efb65f66">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#b878cde2a28128a1ce4a4106b42d1e16efb65f66"><strong>edu/mit/compbio/ChromHMM/BrowserOutput.java</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,8 +159,8 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szColor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szColor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<td class="old_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java">             <span class="n" style="color: #333;">hmcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szID</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">szColor</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java">   <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java">   <span class="n" style="color: #333;">brcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,8 +347,8 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="java">      <span class="n" style="color: #333;">hmlabelExtend</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szID</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szLabelExtend</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="java">   <span class="o" style="font-weight: 600;">}</span>      </span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="java">   <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -378,10 +378,10 @@ public class BrowserOutput</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="new_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="old_line diff-line-num old" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szFullID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szFullID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">//this removes ordering type</span></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="java">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="java">      <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -426,10 +426,10 @@ public class BrowserOutput</td>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szFullID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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431

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="java">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szFullID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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433

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="java">      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">//this removes ordering type</span></span>

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<td class="old_line diff-line-num" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

434

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="java">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>

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435

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435

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="java">      <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -496,10 +496,10 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="java">       <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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497

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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499

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<td class="new_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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500

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<td class="new_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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501

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<pre style="margin: 0;">-<span id="LC501" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

502

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<td class="new_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="java">    <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="java">    <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<td class="new_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

504

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<td class="new_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

504

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<td class="new_line diff-line-num" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="java">    <span class="n" style="color: #333;">hmlabelToFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -740,10 +740,10 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<td class="new_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC740" class="line" lang="java">       <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

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<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

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<pre style="margin: 0;"> <span id="LC741" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

743

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<td class="new_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC743" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

744

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<td class="new_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC744" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

745

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<td class="new_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC745" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

746

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<td class="new_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC746" class="line" lang="java">    <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

743

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<pre style="margin: 0;">+<span id="LC743" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

744

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<pre style="margin: 0;">+<span id="LC744" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

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<pre style="margin: 0;">+<span id="LC745" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

746

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<pre style="margin: 0;">+<span id="LC746" class="line" lang="java">    <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

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<pre style="margin: 0;"> <span id="LC747" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC748" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

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<pre style="margin: 0;"> <span id="LC749" class="line" lang="java">    <span class="n" style="color: #333;">hmlabelToFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -827,12 +827,12 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

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<td class="new_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

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<pre style="margin: 0;"> <span id="LC827" class="line" lang="java">              <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

<td class="new_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

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<pre style="margin: 0;"> <span id="LC828" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

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<td class="new_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

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<pre style="margin: 0;"> <span id="LC829" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

830

</td>

<td class="new_line diff-line-num old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC830" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

831

</td>

<td class="new_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

831

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<pre style="margin: 0;"> <span id="LC831" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="new_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC832" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

833

</td>

<td class="new_line diff-line-num old" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC833" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

834

</td>

<td class="new_line diff-line-num old" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC834" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

835

</td>

<td class="new_line diff-line-num old" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC835" class="line" lang="java">                     <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

833

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<pre style="margin: 0;">+<span id="LC833" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

834

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<pre style="margin: 0;">+<span id="LC834" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

835

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<pre style="margin: 0;">+<span id="LC835" class="line" lang="java">                     <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="new_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

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<pre style="margin: 0;"> <span id="LC836" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

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<td class="new_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

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<pre style="margin: 0;"> <span id="LC837" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

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<td class="new_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

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<pre style="margin: 0;"> <span id="LC838" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -930,12 +930,12 @@ public class BrowserOutput</td>

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<td class="old_line diff-line-num" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

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<td class="new_line diff-line-num" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

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<pre style="margin: 0;"> <span id="LC930" class="line" lang="java">              <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

</td>

<td class="new_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

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<pre style="margin: 0;"> <span id="LC931" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

</td>

<td class="new_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC932" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

933

</td>

<td class="new_line diff-line-num old" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC933" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

933

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC933" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

934

</td>

<td class="new_line diff-line-num" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

934

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC934" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

<td class="new_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC935" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

936

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<td class="new_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC936" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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937

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<td class="new_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC937" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

938

</td>

<td class="new_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC938" class="line" lang="java">              <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

936

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<pre style="margin: 0;">+<span id="LC936" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

937

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<pre style="margin: 0;">+<span id="LC937" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

938

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<pre style="margin: 0;">+<span id="LC938" class="line" lang="java">              <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

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<td class="new_line diff-line-num" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

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<pre style="margin: 0;"> <span id="LC939" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

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<td class="new_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

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<pre style="margin: 0;"> <span id="LC940" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

941

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941

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<pre style="margin: 0;"> <span id="LC941" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<br>

</li>

<li id="e1a765a5b2b828119bc810319c6fa07e7300eecf">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#e1a765a5b2b828119bc810319c6fa07e7300eecf"><strong>edu/mit/compbio/ChromHMM/ChromHMM.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -814,8 +814,8 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

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<td class="new_line diff-line-num" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC814" class="line" lang="java">     <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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</td>

<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

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<pre style="margin: 0;"> <span id="LC815" class="line" lang="java">     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

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<td class="new_line diff-line-num" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC816" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

817

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<td class="new_line diff-line-num old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC817" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

818

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<td class="new_line diff-line-num old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC818" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC817" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

818

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<pre style="margin: 0;">+<span id="LC818" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

</td>

<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="java">         <span class="n" style="color: #333;">hmlabelExtend</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szID</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szLabelExtend</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

</td>

<td class="new_line diff-line-num" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<pre style="margin: 0;"> <span id="LC820" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

</td>

<td class="new_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

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<pre style="margin: 0;"> <span id="LC821" class="line" lang="java">     <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1072,7 +1072,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1072

</td>

<td class="new_line diff-line-num" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1072

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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1073

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<td class="new_line diff-line-num" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1073

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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="java">           <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brstate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1074

</td>

<td class="new_line diff-line-num" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1074

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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1075

</td>

<td class="new_line diff-line-num old" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1075" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1075

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1075" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1076

</td>

<td class="new_line diff-line-num" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1076

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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nold</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

</td>

<td class="new_line diff-line-num" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nnew</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1078

</td>

<td class="new_line diff-line-num" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1078

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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="java">               <span class="n" style="color: #333;">stateordering</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nnew</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nold</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1156,8 +1156,8 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

</td>

<td class="new_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1156" class="line" lang="java">                    <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

</td>

<td class="new_line diff-line-num" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="java">                    <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1158

</td>

<td class="new_line diff-line-num" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1158

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1158" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1159

</td>

<td class="new_line diff-line-num old" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1159" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1160

</td>

<td class="new_line diff-line-num old" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1160" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szinstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1159

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1159" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1160

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1160" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szinstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1161

</td>

<td class="new_line diff-line-num" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1161

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1161" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutstate</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

</td>

<td class="new_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1162" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="new_line diff-line-num" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1163" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinstate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1172,7 +1172,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

</td>

<td class="new_line diff-line-num" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1172" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1173

</td>

<td class="new_line diff-line-num" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1173

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1173" class="line" lang="java">                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1174

</td>

<td class="new_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1174

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1174" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1175

</td>

<td class="new_line diff-line-num old" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1175" class="line" lang="java">                    <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1175

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1175" class="line" lang="java">                    <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1176

</td>

<td class="new_line diff-line-num" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1176

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1176" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1177

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1177

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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="java">                <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1178

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<td class="new_line diff-line-num" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1178

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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1199,8 +1199,8 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1199

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<td class="new_line diff-line-num" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1199

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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="java">                    <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1200

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<td class="new_line diff-line-num" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1200

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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="java">                    <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1201

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<td class="new_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1201

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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1202

</td>

<td class="new_line diff-line-num old" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="java">                <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1203

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<td class="new_line diff-line-num old" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1203" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szinstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1202

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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="java">                <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1203

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1203" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szinstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

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<td class="new_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutstate</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

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<td class="new_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1205" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinstate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1206" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1214,7 +1214,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1214

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<td class="new_line diff-line-num" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1214

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1214" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1215

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<td class="new_line diff-line-num" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1215

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1215" class="line" lang="java">                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1216

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<td class="new_line diff-line-num" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1216

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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1217

</td>

<td class="new_line diff-line-num old" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1217" class="line" lang="java">                    <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1217

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1217" class="line" lang="java">                    <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1218

</td>

<td class="new_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1218

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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1219

</td>

<td class="new_line diff-line-num" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1219

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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="java">                <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1220

</td>

<td class="new_line diff-line-num" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1220

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1220" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1902,7 +1902,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1902

</td>

<td class="new_line diff-line-num" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1902

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<pre style="margin: 0;"> <span id="LC1902" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1903

</td>

<td class="new_line diff-line-num" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1903

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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="java">               <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1904

</td>

<td class="new_line diff-line-num" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1904

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<pre style="margin: 0;"> <span id="LC1904" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1905

</td>

<td class="new_line diff-line-num old" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1905" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1905

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1905" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1906

</td>

<td class="new_line diff-line-num" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1906

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1906" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1907

</td>

<td class="new_line diff-line-num" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1907

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<pre style="margin: 0;"> <span id="LC1907" class="line" lang="java">                </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1908

</td>

<td class="new_line diff-line-num" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1908

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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="java">                  <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1912,7 +1912,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

</td>

<td class="new_line diff-line-num" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1912" class="line" lang="java">                        <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Found line without "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" values in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nseq</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

</td>

<td class="new_line diff-line-num" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

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<pre style="margin: 0;"> <span id="LC1913" class="line" lang="java">                     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1914

</td>

<td class="new_line diff-line-num" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1914

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1914" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1915

</td>

<td class="new_line diff-line-num old" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1915" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1915

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1915" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1916

</td>

<td class="new_line diff-line-num" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1916

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1916" class="line" lang="java">                    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1917

</td>

<td class="new_line diff-line-num" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1917

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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="java">                     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1918

</td>

<td class="new_line diff-line-num" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1918

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1918" class="line" lang="java">                     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2903,13 +2903,13 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2903

</td>

<td class="new_line diff-line-num" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2903

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2903" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLoadHeader</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2904

</td>

<td class="new_line diff-line-num" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2904

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2904" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2905

</td>

<td class="new_line diff-line-num" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2905

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2905" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//first token of the first line of the model file is assume to give the number of states</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2906

</td>

<td class="new_line diff-line-num old" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2906" class="line" lang="java">        <span class="n" style="color: #333;">numstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2907

</td>

<td class="new_line diff-line-num old" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2907" class="line" lang="java">        <span class="n" style="color: #333;">numdatasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2906

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2906" class="line" lang="java">        <span class="n" style="color: #333;">numstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2907

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2907" class="line" lang="java">        <span class="n" style="color: #333;">numdatasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2908

</td>

<td class="new_line diff-line-num" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2908

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<pre style="margin: 0;"> <span id="LC2908" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">datasets</span> <span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2909

</td>

<td class="new_line diff-line-num" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2909

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2909" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC2910" class="line" lang="java">            <span class="n" style="color: #333;">datasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2911" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2912

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<td class="new_line diff-line-num old" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2912" class="line" lang="java">        <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2912" class="line" lang="java">        <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2913" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2914" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">nstateorder</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">STATEORDER_TRANSITION</span><span class="o" style="font-weight: 600;">)&&(</span><span class="n" style="color: #333;">nstateorder</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">STATEORDER_EMISSION</span><span class="o" style="font-weight: 600;">)&&(</span><span class="n" style="color: #333;">nstateorder</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">STATEORDER_FIXED</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

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<td class="new_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2964,20 +2964,20 @@ public class ChromHMM</td>

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<pre style="margin: 0;"> <span id="LC2964" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

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<td class="new_line diff-line-num" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

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<pre style="margin: 0;"> <span id="LC2965" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2966

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<td class="new_line diff-line-num" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2966" class="line" lang="java">            <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2967

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<td class="new_line diff-line-num old" data-linenumber="2967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2967" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szvartype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2967" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szvartype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2968

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<td class="new_line diff-line-num" data-linenumber="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2968

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2968" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2969

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<td class="new_line diff-line-num" data-linenumber="2969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2969

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<pre style="margin: 0;"> <span id="LC2969" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szvartype</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"probinit"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2970

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<td class="new_line diff-line-num" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2970

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<pre style="margin: 0;"> <span id="LC2970" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2971" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">//reading an inital probability</span></span>

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<pre style="margin: 0;">-<span id="LC2972" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC2973" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC2972" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC2973" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="java">                <span class="n" style="color: #333;">probinit</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC2975" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC2976" class="line" lang="java">            <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szvartype</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"transitionprobs"</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC2977" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC2978" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC2979" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nto</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC2980" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC2978" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC2979" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nto</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="2980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2980" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">//this smooths the transition probability if dproceduresmmothtransition>0 using a weighted average with uniform </span></span>

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<pre style="margin: 0;"> <span id="LC2982" class="line" lang="java">                <span class="n" style="color: #333;">transitionprobs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nto</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dproceduresmoothtransition</span><span class="o" style="font-weight: 600;">/((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">transitionprobs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)+(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">dproceduresmoothtransition</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC2983" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">transitionprobs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nto</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2989,20 +2989,20 @@ public class ChromHMM</td>

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<pre style="margin: 0;"> <span id="LC2989" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC2990" class="line" lang="java">            <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szvartype</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"emissionprobs"</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC2991" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC2992" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC2993" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmod</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">-<span id="LC2994" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szdataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC2992" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC2993" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmod</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;">+<span id="LC2994" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szdataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC2995" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">]==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2996

</td>

<td class="new_line diff-line-num" data-linenumber="2996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2996

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<pre style="margin: 0;"> <span id="LC2996" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2997

</td>

<td class="new_line diff-line-num old" data-linenumber="2997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2997" class="line" lang="java">                    <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szdataset</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//st.nextToken();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2997

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<pre style="margin: 0;">+<span id="LC2997" class="line" lang="java">                    <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szdataset</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//st.nextToken()<span class="idiff left right">.trim()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2998

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<td class="new_line diff-line-num" data-linenumber="2998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2998

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<pre style="margin: 0;"> <span id="LC2998" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2999

</td>

<td class="new_line diff-line-num" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2999

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<pre style="margin: 0;"> <span id="LC2999" class="line" lang="java">                <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szdataset</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">]))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3000

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<td class="new_line diff-line-num" data-linenumber="3000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3000

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<pre style="margin: 0;"> <span id="LC3000" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3001

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<td class="new_line diff-line-num" data-linenumber="3001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3001

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<pre style="margin: 0;"> <span id="LC3001" class="line" lang="java">                    <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"For mark "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in model file found "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szdataset</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", but expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">"."</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3002

</td>

<td class="new_line diff-line-num" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3002

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<pre style="margin: 0;"> <span id="LC3002" class="line" lang="java">                                                      <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" This might be because columns of binarized file are in a different order from model learning."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3003

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<td class="new_line diff-line-num" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3003

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<pre style="margin: 0;"> <span id="LC3003" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3004

</td>

<td class="new_line diff-line-num old" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3004" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3005

</td>

<td class="new_line diff-line-num old" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3005" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3004

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3004" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3005

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3005" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3006

</td>

<td class="new_line diff-line-num" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3006

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3006" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">//smooths the emission probability if dproceduresmoothemission>0 using a weighted average with uniform</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3007

</td>

<td class="new_line diff-line-num" data-linenumber="3007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3007

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<pre style="margin: 0;"> <span id="LC3007" class="line" lang="java">                <span class="n" style="color: #333;">emissionprobs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmod</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nval</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dproceduresmoothemission</span><span class="o" style="font-weight: 600;">/((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">numbuckets</span><span class="o" style="font-weight: 600;">)+(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">dproceduresmoothemission</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3008

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<pre style="margin: 0;"> <span id="LC3008" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3229,7 +3229,7 @@ public class ChromHMM</td>

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<pre style="margin: 0;"> <span id="LC3229" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nline</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3230" class="line" lang="java">             <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLinePosterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brprobs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="3231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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3231

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<pre style="margin: 0;"> <span id="LC3231" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3232" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stposterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLinePosterior</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3232" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stposterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLinePosterior</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3233" class="line" lang="java">                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numstates</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3234

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<pre style="margin: 0;"> <span id="LC3234" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3235" class="line" lang="java">                   <span class="n" style="color: #333;">fullposterior</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nline</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3288,13 +3288,13 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="3288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3288" class="line" lang="java">             <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLineMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brbed</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="3289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3289

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<pre style="margin: 0;"> <span id="LC3289" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3290" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineMax</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3291

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<td class="new_line diff-line-num old" data-linenumber="3291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3291" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3291" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3292

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<td class="new_line diff-line-num" data-linenumber="3292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3292" class="line" lang="java"></span>

</pre>

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3293

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<pre style="margin: 0;"> <span id="LC3293" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="old_line diff-line-num" data-linenumber="3294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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3294

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<pre style="margin: 0;"> <span id="LC3294" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3295" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3296" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3297" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span>                                 </span>

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<td class="old_line diff-line-num new" data-linenumber="3298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3295" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3296" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="3298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3297" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span>                                    </span>

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<pre style="margin: 0;"> <span id="LC3298" class="line" lang="java">                     <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegin</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">++)</span></span>

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<td class="old_line diff-line-num" data-linenumber="3299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3299" class="line" lang="java">                     <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="3300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3300" class="line" lang="java">                         <span class="n" style="color: #333;">fullmax</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3990,7 +3990,7 @@ public class ChromHMM</td>

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3990

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3990

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<pre style="margin: 0;"> <span id="LC3990" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3991

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<td class="new_line diff-line-num" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3991

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<pre style="margin: 0;"> <span id="LC3991" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3992

</td>

<td class="new_line diff-line-num" data-linenumber="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3992

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<pre style="margin: 0;"> <span id="LC3992" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3993

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<td class="new_line diff-line-num old" data-linenumber="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3993" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3993

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<pre style="margin: 0;">+<span id="LC3993" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3994

</td>

<td class="new_line diff-line-num" data-linenumber="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3994

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<pre style="margin: 0;"> <span id="LC3994" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3995

</td>

<td class="new_line diff-line-num" data-linenumber="3995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3995

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<pre style="margin: 0;"> <span id="LC3995" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3996

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<td class="new_line diff-line-num" data-linenumber="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3996

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<pre style="margin: 0;"> <span id="LC3996" class="line" lang="java">              <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4000,7 +4000,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4000

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<td class="new_line diff-line-num" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4000

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<pre style="margin: 0;"> <span id="LC4000" class="line" lang="java">                    <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Found line without "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" values in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nordered_nseq</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4001

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<td class="new_line diff-line-num" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4001

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<pre style="margin: 0;"> <span id="LC4001" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4002

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<td class="new_line diff-line-num" data-linenumber="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4002

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<pre style="margin: 0;"> <span id="LC4002" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4003

</td>

<td class="new_line diff-line-num old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4003" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4003

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<pre style="margin: 0;">+<span id="LC4003" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4004

</td>

<td class="new_line diff-line-num" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4004

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4004" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4005

</td>

<td class="new_line diff-line-num" data-linenumber="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4005

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<pre style="margin: 0;"> <span id="LC4005" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4006

</td>

<td class="new_line diff-line-num" data-linenumber="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4006

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<pre style="margin: 0;"> <span id="LC4006" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4138,7 +4138,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="4138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4138

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<td class="new_line diff-line-num" data-linenumber="4138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4138

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<pre style="margin: 0;"> <span id="LC4138" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nline</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4139

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<td class="new_line diff-line-num" data-linenumber="4139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4139

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<pre style="margin: 0;"> <span id="LC4139" class="line" lang="java">             <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLinePosterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brprobs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4140

</td>

<td class="new_line diff-line-num" data-linenumber="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4140

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<pre style="margin: 0;"> <span id="LC4140" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4141

</td>

<td class="new_line diff-line-num old" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4141" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stposterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLinePosterior</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4141

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4141" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stposterior</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLinePosterior</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4142

</td>

<td class="new_line diff-line-num" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4142

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<pre style="margin: 0;"> <span id="LC4142" class="line" lang="java">                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numstates</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4143

</td>

<td class="new_line diff-line-num" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4143

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<pre style="margin: 0;"> <span id="LC4143" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4144

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<td class="new_line diff-line-num" data-linenumber="4144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4144

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<pre style="margin: 0;"> <span id="LC4144" class="line" lang="java">                   <span class="n" style="color: #333;">fullposterior</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nline</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4197,13 +4197,13 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4197

</td>

<td class="new_line diff-line-num" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4197

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4197" class="line" lang="java">             <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLineMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brbed</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4198

</td>

<td class="new_line diff-line-num" data-linenumber="4198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4198

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4198" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4199

</td>

<td class="new_line diff-line-num" data-linenumber="4199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4199

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4199" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineMax</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4200

</td>

<td class="new_line diff-line-num old" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4200" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4200

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4200" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4201

</td>

<td class="new_line diff-line-num" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4201

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4201" class="line" lang="java"></span>

</pre>

</td>

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4202

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4202

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<pre style="margin: 0;"> <span id="LC4202" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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4203

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4203

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<pre style="margin: 0;"> <span id="LC4203" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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4204

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<td class="new_line diff-line-num old" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4204" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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4205

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<td class="new_line diff-line-num old" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4205" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4206

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<td class="new_line diff-line-num old" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4206" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span>                                 </span>

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<td class="old_line diff-line-num new" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4204" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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4205

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<pre style="margin: 0;">+<span id="LC4205" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4206" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span>                                    </span>

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4207

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<pre style="margin: 0;"> <span id="LC4207" class="line" lang="java">                     <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegin</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">++)</span></span>

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4208

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<pre style="margin: 0;"> <span id="LC4208" class="line" lang="java">                     <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC4209" class="line" lang="java">                         <span class="n" style="color: #333;">fullmax</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4983,7 +4983,7 @@ public class ChromHMM</td>

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4983

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4983

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<pre style="margin: 0;"> <span id="LC4983" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

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4984

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<pre style="margin: 0;"> <span id="LC4984" class="line" lang="java">           <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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4985

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<td class="new_line diff-line-num" data-linenumber="4985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4985

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<pre style="margin: 0;"> <span id="LC4985" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="4986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4986" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4986" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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4987

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<pre style="margin: 0;"> <span id="LC4987" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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4988

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4988

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<pre style="margin: 0;"> <span id="LC4988" class="line" lang="java">                </span>

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<pre style="margin: 0;"> <span id="LC4989" class="line" lang="java">              <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5168,12 +5168,12 @@ public class ChromHMM</td>

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<pre style="margin: 0;"> <span id="LC5168" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5169" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cellSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nordered_nseq</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szactualchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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5170

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<td class="new_line diff-line-num" data-linenumber="5170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5170

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<pre style="margin: 0;"> <span id="LC5170" class="line" lang="java">                    <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="5171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5171

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<td class="new_line diff-line-num old" data-linenumber="5171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5171" class="line" lang="java">                    <span class="n" style="color: #333;">pw<span class="idiff left right">probs</span>zip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5171

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<pre style="margin: 0;">+<span id="LC5171" class="line" lang="java">                    <span class="n" style="color: #333;">pw<span class="idiff left">max</span>zip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//fix 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5172

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<td class="new_line diff-line-num" data-linenumber="5172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5172

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<pre style="margin: 0;"> <span id="LC5172" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">//pwmax.println(cellSeq[nordered_nseq]+"\t"+chromSeq[nordered_nseq]);</span></span>

</pre>

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5173

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<td class="new_line diff-line-num" data-linenumber="5173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5173

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<pre style="margin: 0;"> <span id="LC5173" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5174

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<td class="new_line diff-line-num" data-linenumber="5174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5174

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<pre style="margin: 0;"> <span id="LC5174" class="line" lang="java">                    <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MaxState "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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5175

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<td class="new_line diff-line-num" data-linenumber="5175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5175

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<pre style="margin: 0;"> <span id="LC5175" class="line" lang="java">                    <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="5176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5176

</td>

<td class="new_line diff-line-num old" data-linenumber="5176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5176" class="line" lang="java">                    <span class="n" style="color: #333;">pw<span class="idiff left right">probs</span>zip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5176

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5176" class="line" lang="java">                    <span class="n" style="color: #333;">pw<span class="idiff left">max</span>zip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//fix 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5177

</td>

<td class="new_line diff-line-num" data-linenumber="5177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5177

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<pre style="margin: 0;"> <span id="LC5177" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">//pwmax.println("MaxState "+chorder);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5178

</td>

<td class="new_line diff-line-num" data-linenumber="5178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5178

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<pre style="margin: 0;"> <span id="LC5178" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5179

</td>

<td class="new_line diff-line-num" data-linenumber="5179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5179

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5179" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7703,7 +7703,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="7703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7703

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<td class="new_line diff-line-num" data-linenumber="7703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7703

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<pre style="margin: 0;"> <span id="LC7703" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7704

</td>

<td class="new_line diff-line-num" data-linenumber="7704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7704

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<pre style="margin: 0;"> <span id="LC7704" class="line" lang="java">              <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7705

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<td class="new_line diff-line-num" data-linenumber="7705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7705

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<pre style="margin: 0;"> <span id="LC7705" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7706

</td>

<td class="new_line diff-line-num old" data-linenumber="7706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7706" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="7707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7706

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7706" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7707

</td>

<td class="new_line diff-line-num" data-linenumber="7707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7707

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7707" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7708

</td>

<td class="new_line diff-line-num" data-linenumber="7708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7708

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<pre style="margin: 0;"> <span id="LC7708" class="line" lang="java">                </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7709

</td>

<td class="new_line diff-line-num" data-linenumber="7709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7709

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<pre style="margin: 0;"> <span id="LC7709" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7713,7 +7713,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="7713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7713

</td>

<td class="new_line diff-line-num" data-linenumber="7713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7713

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<pre style="margin: 0;"> <span id="LC7713" class="line" lang="java">                       <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Found line without "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" values in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nseq</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7714

</td>

<td class="new_line diff-line-num" data-linenumber="7714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7714

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<pre style="margin: 0;"> <span id="LC7714" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7715

</td>

<td class="new_line diff-line-num" data-linenumber="7715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7715

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7715" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="7716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7716

</td>

<td class="new_line diff-line-num old" data-linenumber="7716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7716" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="7717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7716

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7716" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7717

</td>

<td class="new_line diff-line-num" data-linenumber="7717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7717

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7717" class="line" lang="java">                    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7718

</td>

<td class="new_line diff-line-num" data-linenumber="7718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7718

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<pre style="margin: 0;"> <span id="LC7718" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7719

</td>

<td class="new_line diff-line-num" data-linenumber="7719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7719

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7719" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10265,7 +10265,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="10265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10265

</td>

<td class="new_line diff-line-num" data-linenumber="10265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10265

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<pre style="margin: 0;"> <span id="LC10265" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10266

</td>

<td class="new_line diff-line-num" data-linenumber="10266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10266

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<pre style="margin: 0;"> <span id="LC10266" class="line" lang="java">             <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10267

</td>

<td class="new_line diff-line-num" data-linenumber="10267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10267

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10267" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="10268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10268

</td>

<td class="new_line diff-line-num old" data-linenumber="10268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10268" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="10269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10268

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10268" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10269

</td>

<td class="new_line diff-line-num" data-linenumber="10269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10269

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10269" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10270

</td>

<td class="new_line diff-line-num" data-linenumber="10270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10270

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10270" class="line" lang="java">               </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10271

</td>

<td class="new_line diff-line-num" data-linenumber="10271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10271

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10271" class="line" lang="java">                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10275,7 +10275,7 @@ public class ChromHMM</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10275

</td>

<td class="new_line diff-line-num" data-linenumber="10275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10275

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<pre style="margin: 0;"> <span id="LC10275" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Found line without "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" values in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles_nseq</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10276

</td>

<td class="new_line diff-line-num" data-linenumber="10276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10276

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10276" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10277

</td>

<td class="new_line diff-line-num" data-linenumber="10277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10277

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10277" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="10278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10278

</td>

<td class="new_line diff-line-num old" data-linenumber="10278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10278" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="10279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10278

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10278" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10279

</td>

<td class="new_line diff-line-num" data-linenumber="10279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10279

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10279" class="line" lang="java">                   </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10280

</td>

<td class="new_line diff-line-num" data-linenumber="10280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10280

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<pre style="margin: 0;"> <span id="LC10280" class="line" lang="java">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10281

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<td class="new_line diff-line-num" data-linenumber="10281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10281

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10281" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12286,12 +12286,12 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12286

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<td class="new_line diff-line-num" data-linenumber="12286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12286

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<pre style="margin: 0;"> <span id="LC12286" class="line" lang="java">              <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"First line must contain cell type and chromosome. No entries found."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12287

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<td class="new_line diff-line-num" data-linenumber="12287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12287

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12287" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12288

</td>

<td class="new_line diff-line-num" data-linenumber="12288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12288

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12288" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="12289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12289

</td>

<td class="new_line diff-line-num old" data-linenumber="12289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12289" class="line" lang="java">           <span class="n" style="color: #333;">cellSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left right">;</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="12290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12289

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12289" class="line" lang="java">           <span class="n" style="color: #333;">cellSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">();</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//added trim in version 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12290

</td>

<td class="new_line diff-line-num" data-linenumber="12290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12290

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12290" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="12291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12291

</td>

<td class="new_line diff-line-num" data-linenumber="12291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12291

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12291" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12292

</td>

<td class="new_line diff-line-num" data-linenumber="12292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12292

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12292" class="line" lang="java">               <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"First line must contain cell type and chromosome. Only one entry found."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12293

</td>

<td class="new_line diff-line-num" data-linenumber="12293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12293

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12293" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="12294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="12294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12294" class="line" lang="java">           <span class="n" style="color: #333;">chromSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left right">;</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12294" class="line" lang="java">           <span class="n" style="color: #333;">chromSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">();</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//added trim in version 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12295

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<td class="new_line diff-line-num" data-linenumber="12295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12295

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12295" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12296

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<td class="new_line diff-line-num" data-linenumber="12296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12296" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12297

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<pre style="margin: 0;"> <span id="LC12297" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12312,7 +12312,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12312" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ntoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12313

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<td class="new_line diff-line-num" data-linenumber="12313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12313

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<pre style="margin: 0;"> <span id="LC12313" class="line" lang="java">              <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12314

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<td class="new_line diff-line-num" data-linenumber="12314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12314

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<pre style="margin: 0;"> <span id="LC12314" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12315

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<td class="new_line diff-line-num old" data-linenumber="12315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12315" class="line" lang="java">                 <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12315

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<pre style="margin: 0;">+<span id="LC12315" class="line" lang="java">                 <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12316

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<td class="new_line diff-line-num" data-linenumber="12316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12316

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<pre style="margin: 0;"> <span id="LC12316" class="line" lang="java">                 <span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12317

</td>

<td class="new_line diff-line-num" data-linenumber="12317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12317

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<pre style="margin: 0;"> <span id="LC12317" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="12318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12318

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<td class="new_line diff-line-num" data-linenumber="12318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12318

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<pre style="margin: 0;"> <span id="LC12318" class="line" lang="java">              <span class="c1" style="color: #998; font-style: italic;">//numdatasets is the number of marks we are integrating</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12330,7 +12330,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12330

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<td class="new_line diff-line-num" data-linenumber="12330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12330

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<pre style="margin: 0;"> <span id="LC12330" class="line" lang="java">               <span class="c1" style="color: #998; font-style: italic;">//Gives warning if a header column does not match</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12331

</td>

<td class="new_line diff-line-num" data-linenumber="12331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12331

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<pre style="margin: 0;"> <span id="LC12331" class="line" lang="java">               <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12332

</td>

<td class="new_line diff-line-num" data-linenumber="12332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12332

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<pre style="margin: 0;"> <span id="LC12332" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC12333" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12333" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12334" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12335

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<td class="new_line diff-line-num" data-linenumber="12335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12335" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12336" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"WARNING headers do not match between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" and "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12632,12 +12632,12 @@ public class ChromHMM</td>

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<td class="new_line diff-line-num" data-linenumber="12632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12632" class="line" lang="java">              <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"First line must contain cell type and chromosome. No entries found."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="12633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12633" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12634" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12635

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<td class="new_line diff-line-num old" data-linenumber="12635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12635" class="line" lang="java">           <span class="n" style="color: #333;">cellSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left right">;</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12635" class="line" lang="java">           <span class="n" style="color: #333;">cellSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">();</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//added trim in version 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12636" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12637

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<pre style="margin: 0;"> <span id="LC12637" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12638

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<pre style="margin: 0;"> <span id="LC12638" class="line" lang="java">               <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"First line must contain cell type and chromosome. Only one entry found."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12639" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12640

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<td class="new_line diff-line-num old" data-linenumber="12640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12640" class="line" lang="java">           <span class="n" style="color: #333;">chromSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left right">;</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12640" class="line" lang="java">           <span class="n" style="color: #333;">chromSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">();</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//added trim in version 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12641

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<td class="new_line diff-line-num" data-linenumber="12641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12641

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12641" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12642" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12643

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<td class="new_line diff-line-num" data-linenumber="12643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12643

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<pre style="margin: 0;"> <span id="LC12643" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12658,7 +12658,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12658" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ntoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12659" class="line" lang="java">              <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12660" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12661

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<td class="new_line diff-line-num old" data-linenumber="12661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12661" class="line" lang="java">                 <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12661

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<pre style="margin: 0;">+<span id="LC12661" class="line" lang="java">                 <span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12662

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<td class="new_line diff-line-num" data-linenumber="12662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12662

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<pre style="margin: 0;"> <span id="LC12662" class="line" lang="java">                 <span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="12663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12663" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12664

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<td class="new_line diff-line-num" data-linenumber="12664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12664

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<pre style="margin: 0;"> <span id="LC12664" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12674,7 +12674,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12674

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<td class="new_line diff-line-num" data-linenumber="12674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12674

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<pre style="margin: 0;"> <span id="LC12674" class="line" lang="java">               <span class="c1" style="color: #998; font-style: italic;">//Gives warning if a header column does not match</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12675

</td>

<td class="new_line diff-line-num" data-linenumber="12675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12675

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12675" class="line" lang="java">               <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12676

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<td class="new_line diff-line-num" data-linenumber="12676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12676" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12677

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<td class="new_line diff-line-num old" data-linenumber="12677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12677" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12677

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12677" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12678

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<td class="new_line diff-line-num" data-linenumber="12678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12678

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<pre style="margin: 0;"> <span id="LC12678" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ntoken</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12679

</td>

<td class="new_line diff-line-num" data-linenumber="12679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12679

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<pre style="margin: 0;"> <span id="LC12679" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12680

</td>

<td class="new_line diff-line-num" data-linenumber="12680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12680

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<pre style="margin: 0;"> <span id="LC12680" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"WARNING headers do not match between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" and "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12689,7 +12689,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12689

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<td class="new_line diff-line-num" data-linenumber="12689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12689

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<pre style="margin: 0;"> <span id="LC12689" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">aldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12690

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<td class="new_line diff-line-num" data-linenumber="12690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12690

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<pre style="margin: 0;"> <span id="LC12690" class="line" lang="java">           <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12691

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<td class="new_line diff-line-num" data-linenumber="12691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12691

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<pre style="margin: 0;"> <span id="LC12691" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="12692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12692

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<td class="new_line diff-line-num old" data-linenumber="12692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12692" class="line" lang="java">               <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12692

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12692" class="line" lang="java">               <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12693

</td>

<td class="new_line diff-line-num" data-linenumber="12693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12693

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<pre style="margin: 0;"> <span id="LC12693" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12694

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<td class="new_line diff-line-num" data-linenumber="12694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12694

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<pre style="margin: 0;"> <span id="LC12694" class="line" lang="java">               </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12695

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<td class="new_line diff-line-num" data-linenumber="12695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12695

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<pre style="margin: 0;"> <span id="LC12695" class="line" lang="java">               <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12700,7 +12700,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="12700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12700

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<td class="new_line diff-line-num" data-linenumber="12700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12700

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<pre style="margin: 0;"> <span id="LC12700" class="line" lang="java">                       <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Found line without "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numdatasets</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" values in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">chromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12701

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<td class="new_line diff-line-num" data-linenumber="12701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12701

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<pre style="margin: 0;"> <span id="LC12701" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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12702

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12702

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<pre style="margin: 0;"> <span id="LC12702" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12703

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<td class="new_line diff-line-num old" data-linenumber="12703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12703" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12703

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<pre style="margin: 0;">+<span id="LC12703" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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12704

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12704

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<pre style="margin: 0;"> <span id="LC12704" class="line" lang="java">                   </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12705

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<pre style="margin: 0;"> <span id="LC12705" class="line" lang="java">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztoken</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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12706

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<td class="new_line diff-line-num" data-linenumber="12706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12706

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<pre style="margin: 0;"> <span id="LC12706" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12848,13 +12848,14 @@ public class ChromHMM</td>

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12848

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<pre style="margin: 0;"> <span id="LC12848" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12849" class="line" lang="java">       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Version"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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12850

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12850

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<pre style="margin: 0;"> <span id="LC12850" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12851

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<td class="new_line diff-line-num old" data-linenumber="12851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12851" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"This is Version 1.2<span class="idiff left right">2</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12851

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<pre style="margin: 0;">+<span id="LC12851" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"This is Version 1.2<span class="idiff left right">3</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12852

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<td class="new_line diff-line-num" data-linenumber="12852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12852

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12852" class="line" lang="java">       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12853

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<td class="new_line diff-line-num" data-linenumber="12853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12853

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<pre style="margin: 0;"> <span id="LC12853" class="line" lang="java">        <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">))||(</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBed"</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12854

</td>

<td class="new_line diff-line-num" data-linenumber="12854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12854

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12854" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12855

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<td class="new_line diff-line-num" data-linenumber="12855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12855

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<pre style="margin: 0;"> <span id="LC12855" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bstacked</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12856

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<td class="new_line diff-line-num" data-linenumber="12856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12856

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<pre style="margin: 0;"> <span id="LC12856" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bgzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12857

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<td class="new_line diff-line-num" data-linenumber="12857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12857

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<pre style="margin: 0;"> <span id="LC12857" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpairend</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12858

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<pre style="margin: 0;">+<span id="LC12858" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bmixed</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12858

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<td class="new_line diff-line-num" data-linenumber="12859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12859

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<pre style="margin: 0;"> <span id="LC12859" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bsplit</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12859

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<td class="new_line diff-line-num" data-linenumber="12860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12860

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<pre style="margin: 0;"> <span id="LC12860" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcontroldir</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12860

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<td class="new_line diff-line-num" data-linenumber="12861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12861

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<pre style="margin: 0;"> <span id="LC12861" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nflankwidthcontrol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13012,6 +13013,10 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="13012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13012

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<td class="new_line diff-line-num" data-linenumber="13013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13013

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<pre style="margin: 0;"> <span id="LC13013" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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13013

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<td class="new_line diff-line-num" data-linenumber="13014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13014

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<pre style="margin: 0;"> <span id="LC13014" class="line" lang="java">                        <span class="n" style="color: #333;">bpairend</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13014

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<td class="new_line diff-line-num" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13015

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<pre style="margin: 0;"> <span id="LC13015" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13016

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<pre style="margin: 0;">+<span id="LC13016" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-mixed"</span><span class="o" style="font-weight: 600;">))&&(</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13017

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<pre style="margin: 0;">+<span id="LC13017" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13018

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<pre style="margin: 0;">+<span id="LC13018" class="line" lang="java">                        <span class="n" style="color: #333;">bmixed</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13019

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<pre style="margin: 0;">+<span id="LC13019" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13015

</td>

<td class="new_line diff-line-num" data-linenumber="13020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13020

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<pre style="margin: 0;"> <span id="LC13020" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-w"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13016

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<td class="new_line diff-line-num" data-linenumber="13021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13021

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13021" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13017

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<td class="new_line diff-line-num" data-linenumber="13022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13022

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13022" class="line" lang="java">                       <span class="n" style="color: #333;">nflankwidthcontrol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[++</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13030,7 +13035,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="13030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13030

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<td class="new_line diff-line-num" data-linenumber="13035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13035

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<pre style="margin: 0;"> <span id="LC13035" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span>              </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13031

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<td class="new_line diff-line-num" data-linenumber="13036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13036

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<pre style="margin: 0;"> <span id="LC13036" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13032

</td>

<td class="new_line diff-line-num" data-linenumber="13037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13037

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13037" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="13033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13033

</td>

<td class="new_line diff-line-num old" data-linenumber="13038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13033" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">bshift</span><span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="13034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13038

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13038" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">bmixed</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">bshift</span><span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13034

</td>

<td class="new_line diff-line-num" data-linenumber="13039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13039

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13039" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13035

</td>

<td class="new_line diff-line-num" data-linenumber="13040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13040

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13040" class="line" lang="java">               <span class="n" style="color: #333;">bok</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13036

</td>

<td class="new_line diff-line-num" data-linenumber="13041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13041

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13041" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13214,7 +13219,7 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="13214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13214

</td>

<td class="new_line diff-line-num" data-linenumber="13219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13219

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13219" class="line" lang="java">                                               <span class="n" style="color: #333;">szoutputbinarydirsub</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutputcontroldir</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13215

</td>

<td class="new_line diff-line-num" data-linenumber="13220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13220

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13220" class="line" lang="java">                                               <span class="n" style="color: #333;">dpoissonthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dfoldthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bcontainsthresh</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13216

</td>

<td class="new_line diff-line-num" data-linenumber="13221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13221

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13221" class="line" lang="java">                                               <span class="n" style="color: #333;">npseudocountcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dcountthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="13217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13217

</td>

<td class="new_line diff-line-num old" data-linenumber="13222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13217" class="line" lang="java">                                       <span class="idiff left right">  </span>     <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numsplitbins</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bstacked</span><span class="o" style="font-weight: 600;">);</span>                  </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="13218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13222

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13222" class="line" lang="java">                                       <span class="idiff left">               </span>     <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numsplitbins</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bstacked</span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bmixed</span></span><span class="o" style="font-weight: 600;">);</span>                     </span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13218

</td>

<td class="new_line diff-line-num" data-linenumber="13223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13223

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13223" class="line" lang="java">                     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13219

</td>

<td class="new_line diff-line-num" data-linenumber="13224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13224

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13224" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13220

</td>

<td class="new_line diff-line-num" data-linenumber="13225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13225

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13225" class="line" lang="java">                 <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13267,7 +13272,7 @@ public class ChromHMM</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="13267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13267

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<td class="new_line diff-line-num" data-linenumber="13272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13272" class="line" lang="java">                                               <span class="n" style="color: #333;">szoutputbinarydir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutputcontroldir</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13268

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<td class="new_line diff-line-num" data-linenumber="13273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13273

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<pre style="margin: 0;"> <span id="LC13273" class="line" lang="java">                                               <span class="n" style="color: #333;">dpoissonthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dfoldthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bcontainsthresh</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13269

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<td class="new_line diff-line-num" data-linenumber="13274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13274

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<pre style="margin: 0;"> <span id="LC13274" class="line" lang="java">                                               <span class="n" style="color: #333;">npseudocountcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dcountthresh</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13270

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<td class="new_line diff-line-num old" data-linenumber="13275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13270" class="line" lang="java">                                       <span class="idiff left right">       </span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numsplitbins</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bstacked</span><span class="o" style="font-weight: 600;">);</span>                    </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13275

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<pre style="margin: 0;">+<span id="LC13275" class="line" lang="java">                                       <span class="idiff left">               </span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numsplitbins</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bstacked</span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">bmixed</span></span><span class="o" style="font-weight: 600;">);</span>                      </span>

</pre>

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13271

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<td class="new_line diff-line-num" data-linenumber="13276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13276

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<pre style="margin: 0;"> <span id="LC13276" class="line" lang="java">                  </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13277

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<pre style="margin: 0;"> <span id="LC13277" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13273

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<td class="new_line diff-line-num" data-linenumber="13278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13278

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<pre style="margin: 0;"> <span id="LC13278" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13291,7 +13296,7 @@ public class ChromHMM</td>

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<td class="new_line diff-line-num" data-linenumber="13296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13296

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<pre style="margin: 0;"> <span id="LC13296" class="line" lang="java">              <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13297" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13298

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<pre style="margin: 0;"> <span id="LC13298" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"usage BinarizeBam [-b binsize][-c controldir][-e offsetend][-f foldthresh]"</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13294

</td>

<td class="new_line diff-line-num old" data-linenumber="13299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13294" class="line" lang="java">                                  <span class="s" style="color: #d14;">"[-g signalthresh][-gzip][[-o outputcontroldir][-p poissonthresh][-paired|[-center][-n shift][-peaks [-i splitindex]]"</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13299

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13299" class="line" lang="java">                                  <span class="s" style="color: #d14;">"[-g signalthresh][-gzip][[-o outputcontroldir][-p poissonthresh][-paired|[-<span class="idiff left right">mixed][-</span>center][-n shift][-peaks [-i splitindex]]"</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13295

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<td class="new_line diff-line-num" data-linenumber="13300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13300

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<pre style="margin: 0;"> <span id="LC13300" class="line" lang="java">                                  <span class="s" style="color: #d14;">"[-s offsetstart][-splitcols [-k splitcolindex][-m numsplitcols]][-splitrows [-j numsplitbins]][-stacked][-strictthresh][-t outputsignaldir]"</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13296

</td>

<td class="new_line diff-line-num" data-linenumber="13301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13301

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<pre style="margin: 0;"> <span id="LC13301" class="line" lang="java">                                  <span class="s" style="color: #d14;">"[-u pseudocountcontrol][-w flankwidthcontrol] "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13297

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<td class="new_line diff-line-num" data-linenumber="13302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13302

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13302" class="line" lang="java">                                     <span class="s" style="color: #d14;">"chromosomelengthfile inputbamdir cellmarkfiletable outputbinarydir"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13541,9 +13546,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="13541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13541

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<pre style="margin: 0;"> <span id="LC13546" class="line" lang="java">                       <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC13547" class="line" lang="java">                       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="13543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13543

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<td class="new_line diff-line-num" data-linenumber="13548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13548

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<pre style="margin: 0;"> <span id="LC13548" class="line" lang="java">                       <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="13544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13544

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<td class="new_line diff-line-num old" data-linenumber="13549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13544" class="line" lang="java">                          <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13545

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<td class="new_line diff-line-num old" data-linenumber="13549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13545" class="line" lang="java">                          <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13546

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<td class="new_line diff-line-num old" data-linenumber="13549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13546" class="line" lang="java">                          <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="old_line diff-line-num new" data-linenumber="13547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13549

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<pre style="margin: 0;">+<span id="LC13549" class="line" lang="java">                          <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="13547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13550

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<pre style="margin: 0;">+<span id="LC13550" class="line" lang="java">                          <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13551

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<pre style="margin: 0;">+<span id="LC13551" class="line" lang="java">                          <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13547

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<td class="new_line diff-line-num" data-linenumber="13552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13552

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<pre style="margin: 0;"> <span id="LC13552" class="line" lang="java">                       <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="13548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13548

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<td class="new_line diff-line-num" data-linenumber="13553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13553

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<pre style="margin: 0;"> <span id="LC13553" class="line" lang="java">                       <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13549

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<td class="new_line diff-line-num" data-linenumber="13554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13554

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<pre style="margin: 0;"> <span id="LC13554" class="line" lang="java">                       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13659,9 +13664,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="13659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13659

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<td class="new_line diff-line-num" data-linenumber="13664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13664

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<pre style="margin: 0;"> <span id="LC13664" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13660

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<td class="new_line diff-line-num" data-linenumber="13665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13665

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<pre style="margin: 0;"> <span id="LC13665" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

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13661

</td>

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13666

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<pre style="margin: 0;"> <span id="LC13666" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13662

</td>

<td class="new_line diff-line-num old" data-linenumber="13667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC13662" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13663

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<td class="new_line diff-line-num old" data-linenumber="13667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13663" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13664

</td>

<td class="new_line diff-line-num old" data-linenumber="13667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13664" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13667

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<pre style="margin: 0;">+<span id="LC13667" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13668

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<pre style="margin: 0;">+<span id="LC13668" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="13665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13669

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<pre style="margin: 0;">+<span id="LC13669" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13665

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<td class="new_line diff-line-num" data-linenumber="13670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13670

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<pre style="margin: 0;"> <span id="LC13670" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13666

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<td class="new_line diff-line-num" data-linenumber="13671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13671

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<pre style="margin: 0;"> <span id="LC13671" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13667

</td>

<td class="new_line diff-line-num" data-linenumber="13672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13672

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13672" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14039,9 +14044,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="14039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14039

</td>

<td class="new_line diff-line-num" data-linenumber="14044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14044

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14044" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14040

</td>

<td class="new_line diff-line-num" data-linenumber="14045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14045

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<pre style="margin: 0;"> <span id="LC14045" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14041

</td>

<td class="new_line diff-line-num" data-linenumber="14046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14046

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14046" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="14042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14042

</td>

<td class="new_line diff-line-num old" data-linenumber="14047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14042" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14043

</td>

<td class="new_line diff-line-num old" data-linenumber="14047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC14043" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14044

</td>

<td class="new_line diff-line-num old" data-linenumber="14047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14044" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="14045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14047

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<pre style="margin: 0;">+<span id="LC14047" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="14045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14048

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<pre style="margin: 0;">+<span id="LC14048" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="14045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14049

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<pre style="margin: 0;">+<span id="LC14049" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14045

</td>

<td class="new_line diff-line-num" data-linenumber="14050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14050

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<pre style="margin: 0;"> <span id="LC14050" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14046

</td>

<td class="new_line diff-line-num" data-linenumber="14051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14051

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<pre style="margin: 0;"> <span id="LC14051" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14047

</td>

<td class="new_line diff-line-num" data-linenumber="14052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14052

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14052" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14211,9 +14216,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="14211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14211

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<td class="new_line diff-line-num" data-linenumber="14216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14216

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<pre style="margin: 0;"> <span id="LC14216" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14212

</td>

<td class="new_line diff-line-num" data-linenumber="14217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14217

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<pre style="margin: 0;"> <span id="LC14217" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="14213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14213

</td>

<td class="new_line diff-line-num" data-linenumber="14218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14218

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14218" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="14214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14214

</td>

<td class="new_line diff-line-num old" data-linenumber="14219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14214" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="14215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14215

</td>

<td class="new_line diff-line-num old" data-linenumber="14219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14215" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="14216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14216

</td>

<td class="new_line diff-line-num old" data-linenumber="14219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14216" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="14217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14219

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<pre style="margin: 0;">+<span id="LC14219" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="14217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14220

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<pre style="margin: 0;">+<span id="LC14220" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="14217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14221

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<pre style="margin: 0;">+<span id="LC14221" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14217

</td>

<td class="new_line diff-line-num" data-linenumber="14222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14222

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<pre style="margin: 0;"> <span id="LC14222" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="14218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14218

</td>

<td class="new_line diff-line-num" data-linenumber="14223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14223

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<pre style="margin: 0;"> <span id="LC14223" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14219

</td>

<td class="new_line diff-line-num" data-linenumber="14224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14224

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14224" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14404,9 +14409,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="14404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14404

</td>

<td class="new_line diff-line-num" data-linenumber="14409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14409

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<pre style="margin: 0;"> <span id="LC14409" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14405

</td>

<td class="new_line diff-line-num" data-linenumber="14410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14410

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<pre style="margin: 0;"> <span id="LC14410" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="14406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14406

</td>

<td class="new_line diff-line-num" data-linenumber="14411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14411

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14411" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="14407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14407

</td>

<td class="new_line diff-line-num old" data-linenumber="14412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14407" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="14408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14408

</td>

<td class="new_line diff-line-num old" data-linenumber="14412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14408" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="14409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14409

</td>

<td class="new_line diff-line-num old" data-linenumber="14412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14409" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="14410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14412

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14412" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="14410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14413

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14413" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="14410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14414

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14414" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14410

</td>

<td class="new_line diff-line-num" data-linenumber="14415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14415

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14415" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14411

</td>

<td class="new_line diff-line-num" data-linenumber="14416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14416

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14416" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14412

</td>

<td class="new_line diff-line-num" data-linenumber="14417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14417

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14417" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14996,9 +15001,9 @@ public class ChromHMM</td>

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<td class="old_line diff-line-num" data-linenumber="14996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14996

</td>

<td class="new_line diff-line-num" data-linenumber="15001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15001

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15001" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14997

</td>

<td class="new_line diff-line-num" data-linenumber="15002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15002

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15002" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14998

</td>

<td class="new_line diff-line-num" data-linenumber="15003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15003

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15003" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14999

</td>

<td class="new_line diff-line-num old" data-linenumber="15004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14999" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15000

</td>

<td class="new_line diff-line-num old" data-linenumber="15004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15000" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="15001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15001

</td>

<td class="new_line diff-line-num old" data-linenumber="15004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15001" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="15002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15004

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15004" class="line" lang="java">                       <span class="n" style="color: #333;">nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="15002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15005

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15005" class="line" lang="java">                       <span class="n" style="color: #333;">ng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="15002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15006

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15006" class="line" lang="java">                       <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="15002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15002

</td>

<td class="new_line diff-line-num" data-linenumber="15007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15007

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15007" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="15003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15003

</td>

<td class="new_line diff-line-num" data-linenumber="15008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15008

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15008" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="15004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15004

</td>

<td class="new_line diff-line-num" data-linenumber="15009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15009

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15009" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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</li>

<li id="c4dd7be4883f31af6f5731277ba2f3147cd4b40a">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#c4dd7be4883f31af6f5731277ba2f3147cd4b40a"><strong>edu/mit/compbio/ChromHMM/ConvertGeneTable.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,37 +140,37 @@ public class ConvertGeneTable</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szbin</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szname</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

151

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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC152" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szstrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC154" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC155" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztxStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztxStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC156" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">sztxStart</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

157

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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC157" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC158" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztxEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC158" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztxEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">sztxEnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<td class="new_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

161

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<td class="new_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcdsStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcdsStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<td class="new_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szcdsStart</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcdsEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcdsEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szcdsEnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC166" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC167" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC166" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szexonCount</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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169

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

170

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonStarts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonStarts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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172

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<td class="new_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonEnds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java">         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonEnds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java">     <span class="c1" style="color: #998; font-style: italic;">//removed 1.22</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">     <span class="c1" style="color: #998; font-style: italic;">//if (!szexonEnds.equals("\t"))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -288,7 +288,7 @@ public class ConvertGeneTable</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonEnds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonEnds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">hsexon</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szexonOut</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szexonOut</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,7 +340,7 @@ public class ConvertGeneTable</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonEnds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szexonOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stexonEnds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">hsexon</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szexonOut</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="new_line diff-line-num" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

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<br>

</li>

<li id="6cf51526a9e3e36b9a53742e82b9e0ea219c57fc">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#6cf51526a9e3e36b9a53742e82b9e0ea219c57fc"><strong>edu/mit/compbio/ChromHMM/NestedEliminateInitialize.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,10 +80,10 @@ public class NestedEliminateInitialize</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"emission"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stemiss</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java">                    <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stemiss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java">                    </span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">Object</span> <span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szmark</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,10 +140,10 @@ public class NestedEliminateInitialize</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"emissionprobs"</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java">               <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java">               <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java">               <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java">               <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java">               <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="n" style="color: #333;">intMark</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szmark</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">intMark</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,10 +154,10 @@ public class NestedEliminateInitialize</td>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java">                   <span class="n" style="color: #333;">nmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">intMark</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szbucket</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<td class="new_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java">                  <span class="n" style="color: #333;">modelemissions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmodel</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="old_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java">                  <span class="n" style="color: #333;">modelemissions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nmodel</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="new_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java">                  <span class="n" style="color: #333;">ncount</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -197,9 +197,9 @@ public class NestedEliminateInitialize</td>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java">        <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinputdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmainfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is missing lines!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinitline</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java">           <span class="n" style="color: #333;">bestprobinit</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java">           <span class="n" style="color: #333;">bestprobinit</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ni</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nbestnumstates</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -212,10 +212,10 @@ public class NestedEliminateInitialize</td>

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<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java">           <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinputdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmainfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is missing lines!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java">       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java">       <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sztransitionline</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java">       <span class="n" style="color: #333;">besttransitionprobs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java">       <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java">       <span class="n" style="color: #333;">besttransitionprobs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -228,9 +228,9 @@ public class NestedEliminateInitialize</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="java">           <span class="n" style="color: #333;">emissionsline</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java">           <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java">           <span class="n" style="color: #333;">emissionsline</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="java">        <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="java"></span>

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<li id="7e91b8c750d2f1f3056fc7dcbd7d4d639572d170">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#7e91b8c750d2f1f3056fc7dcbd7d4d639572d170"><strong>edu/mit/compbio/ChromHMM/Preprocessing.java</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * ChromHMM - automating chromatin state discovery and characterization</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (C) 2008-2012 Massachusetts Institute of Technology</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +88,8 @@ public class Preprocessing</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadGrid</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][][]</span> <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bpresentmarks</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">marks</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nshift</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmfiles</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">,</span> </span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ninitval</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bcontrol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ninitval</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bcontrol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span> </span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bmixed</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nummarks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">  <span class="c1" style="color: #998; font-style: italic;">//initalizes all values in grid to ninitval</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -122,12 +122,12 @@ public class Preprocessing</td>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java">             <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" invalid number of column fields in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" expecting 3 or 4 integers"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java">          <span class="n" style="color: #333;">nchromcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java">          <span class="n" style="color: #333;">nbegincol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java">          <span class="n" style="color: #333;">nendcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java">          <span class="n" style="color: #333;">nchromcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java">          <span class="n" style="color: #333;">nbegincol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java">          <span class="n" style="color: #333;">nendcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java">             <span class="n" style="color: #333;">nstrandcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java">             <span class="n" style="color: #333;">nstrandcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="java">   <span class="n" style="color: #333;">nmaxindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nchromcol</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbegincol</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcol</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nstrandcol</span><span class="o" style="font-weight: 600;">)));</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +195,133 @@ public class Preprocessing</td>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">SamReader</span> <span class="n" style="color: #333;">samReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">srf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">open</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">));</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">SAMRecordIterator</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bmixed</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//added in v1.23 to handle mixed</span></span>

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java">                 <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span></span>

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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;">SAMRecord</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"></span>

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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="java">                    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadPairedFlag</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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206

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

207

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java">                       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProperPairFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFirstOfPairFlag</span><span class="o" style="font-weight: 600;">()&&(!</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">()))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java">                       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstartorig</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAlignmentStart</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendorig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAlignmentEnd</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java">                          <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReferenceName</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bnegstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadNegativeStrandFlag</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ninsertsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInferredInsertSize</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java">                          <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java">                          <span class="c1" style="color: #998; font-style: italic;">//if we don't have the chromosome for the read will ignore it</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java">                          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java">                             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">objInt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java">                             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java">                             <span class="c1" style="color: #998; font-style: italic;">//no center mode in paired end</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java">                             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bnegstrand</span><span class="o" style="font-weight: 600;">)</span> </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span>             </span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//"-"   </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//was nshift</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="java">                                <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ninsertsize</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span>   </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//ninsertsize can be negative so adding</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java">                                       <span class="c1" style="color: #998; font-style: italic;">//removed one from here may need it for backwards consistency                                                     </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java">                             <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//"+"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//was nshift</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java">                                <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nstartorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ninsertsize</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="java">                              <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="java">            </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="java">                             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)&&(</span><span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//increment bin count if falls into valid interval</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java">                                <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">]++;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//we do have this chromosome</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java">                                <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span>                       </span>

</pre>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java">                                <span class="n" style="color: #333;">bdatafound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java">                          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java">                       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="java">                       <span class="c1" style="color: #998; font-style: italic;">//treat it as single end</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="java">                       <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstartorig</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAlignmentStart</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="java">                       <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendorig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAlignmentEnd</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="java">                       <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReferenceName</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="java">                       <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bnegstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadNegativeStrandFlag</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="java">                       <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bunmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java">                       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bunmapped</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="java">                       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="java">                          <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java">                       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="java">                       <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="java">                       <span class="c1" style="color: #998; font-style: italic;">//if we don't have the chromosome for the read will ignore it</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="java">                       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java">                       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">objInt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java">                          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java">                             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,(</span><span class="n" style="color: #333;">nstartorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">);</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="java">                             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">);</span>               </span>

</pre>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="java">                             <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//increment bin count if falls into valid interval</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="java">                                <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">]++;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//we do have this chromosome</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="java">                                <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span>                       </span>

</pre>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="java">                                <span class="n" style="color: #333;">bdatafound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="java">                          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="java">                          <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="java">                          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="java">                             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//uses the center of the interval which is useful if read is already extended</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="java">                                <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nstartorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nendorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">)/(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

296

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="java">                             <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

297

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

298

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bnegstrand</span><span class="o" style="font-weight: 600;">)</span> </span>

</pre>

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299

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="java">                                <span class="o" style="font-weight: 600;">{</span>                  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="java">                                   <span class="c1" style="color: #998; font-style: italic;">//"-"   </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="java">                                   <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nshift</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span>     </span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="java">                                          <span class="c1" style="color: #998; font-style: italic;">//removed one from here may need it for backwards consistency                                                          </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java">                                <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="java">                                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="java">                                   <span class="c1" style="color: #998; font-style: italic;">//"+"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="java">                                   <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nstartorig</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nshift</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java">            </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="java">                             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)&&(</span><span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="java">                             <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//increment bin count if falls into valid interval</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

314

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="java">                                <span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">]++;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">//we do have this chromosome</span></span>

</pre>

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316

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="java">                                <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span>                       </span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="java">                                <span class="n" style="color: #333;">bdatafound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="java">                             <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="java">                          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="java">                       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span>                     </span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="java">              <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java">                 <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -411,7 +537,7 @@ public class Preprocessing</td>

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411

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537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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<pre style="margin: 0;"> <span id="LC538" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Empty line found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

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414

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<td class="new_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

415

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<td class="new_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="n" style="color: #333;">objInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

416

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<td class="new_line diff-line-num" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="java"></span>

</pre>

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417

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<td class="new_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">//if we don't have the chromosome for the read will ignore it</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -423,13 +549,13 @@ public class Preprocessing</td>

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423

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<td class="new_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

549

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="java">                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Missing begin coordinate in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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424

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<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="java">                      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

425

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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

426

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<td class="new_line diff-line-num old" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

552

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC552" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

427

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<td class="new_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

553

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC553" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

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<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

554

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="java">                      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

429

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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="java">                      <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

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<td class="new_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC556" class="line" lang="java">                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Missing end coordinate in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

431

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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC557" class="line" lang="java">                      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

432

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<td class="new_line diff-line-num old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="java">                      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

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<td class="old_line diff-line-num" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

433

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<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="java">                      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

434

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<td class="new_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

435

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<td class="new_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="java">                      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -460,11 +586,11 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

460

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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="java">                               <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"strand column expected, but not found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

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461

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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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<pre style="margin: 0;"> <span id="LC587" class="line" lang="java">                            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

462

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<td class="new_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="java">                            <span class="c1" style="color: #998; font-style: italic;">//looks for strand in sixth column or last column if less than six</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

463

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<td class="new_line diff-line-num old" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="java">                            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="java">                            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

464

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<td class="new_line diff-line-num" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="java">                            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

465

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<td class="new_line diff-line-num old" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="java"> <span class="idiff left right">                       </span>       <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC591" class="line" lang="java"> <span class="idiff left">                       </span>       <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

466

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<td class="new_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

592

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="java">                            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

467

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<td class="new_line diff-line-num old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="java"> <span class="idiff left right">                        </span>       <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="java"> <span class="idiff left">                       </span>       <span class="n" style="color: #333;">szstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

468

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<td class="new_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="java">                                       </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

469

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<td class="new_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="java">                            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szstrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"+"</span><span class="o" style="font-weight: 600;">))</span></span>

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470

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596

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="java">                            <span class="o" style="font-weight: 600;">{</span>                 </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -548,13 +674,13 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

548

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674

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<pre style="margin: 0;"> <span id="LC674" class="line" lang="java">     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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549

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<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="java">         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"empty line found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szchromlengthfile</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

551

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<td class="new_line diff-line-num old" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC551" class="line" lang="java">     <span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="java">     <span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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552

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<td class="new_line diff-line-num" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

678

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<pre style="margin: 0;"> <span id="LC678" class="line" lang="java"></span>

</pre>

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553

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679

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<pre style="margin: 0;"> <span id="LC679" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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554

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680

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<pre style="margin: 0;"> <span id="LC680" class="line" lang="java">     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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555

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681

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="java">         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"missing chromosome length for "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">allines</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szchromlengthfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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556

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682

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

557

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<td class="new_line diff-line-num old" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC557" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

683

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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<td class="new_line diff-line-num" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

684

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<pre style="margin: 0;"> <span id="LC684" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numbins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nlength</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<td class="new_line diff-line-num" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

685

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<pre style="margin: 0;"> <span id="LC685" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//if (nlength % nbinsize !=0)  //removed pre 1.18 to be consistent from binarizing directly</span></span>

</pre>

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560

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686

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//    numbins++;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -606,7 +732,12 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

</td>

<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

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<pre style="margin: 0;"> <span id="LC732" class="line" lang="java">           <span class="n" style="color: #333;">alfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

607

</td>

<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

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<pre style="margin: 0;"> <span id="LC733" class="line" lang="java">           <span class="n" style="color: #333;">hmfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmark</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

</td>

<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

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<pre style="margin: 0;"> <span id="LC734" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

609

</td>

<td class="new_line diff-line-num old" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC609" class="line" lang="java">        <span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC735" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC736" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

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<pre style="margin: 0;">+<span id="LC737" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

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<pre style="margin: 0;">+<span id="LC738" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//added in v1.23 to only count once a given file</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

739

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC739" class="line" lang="java">           <span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

740

</td>

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<pre style="margin: 0;">+<span id="LC740" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

</td>

<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC741" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="java">     <span class="n" style="color: #333;">ncellmarkentry</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

</td>

<td class="new_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC743" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -675,11 +806,11 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

</td>

<td class="new_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC806" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

</td>

<td class="new_line diff-line-num" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC807" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

</td>

<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC808" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

678

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<td class="new_line diff-line-num old" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

809

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

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<td class="new_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

680

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<td class="new_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

681

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<td class="new_line diff-line-num old" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC681" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

682

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<td class="new_line diff-line-num old" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC682" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//updated -1 from pre-release 1.18</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

812

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<pre style="margin: 0;">+<span id="LC812" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

813

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<pre style="margin: 0;">+<span id="LC813" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//updated -1 from pre-release 1.18</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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<td class="new_line diff-line-num" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

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<pre style="margin: 0;"> <span id="LC814" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

684

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<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

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<pre style="margin: 0;"> <span id="LC815" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">//need to update</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

685

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<td class="new_line diff-line-num" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

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<pre style="margin: 0;"> <span id="LC816" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nactualbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -854,7 +985,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

</td>

<td class="new_line diff-line-num" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

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<pre style="margin: 0;"> <span id="LC985" class="line" lang="java">                                      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dpoissonthresh</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dfoldthresh</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bcontainsthresh</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">npseudocountcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

855

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<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC986" class="line" lang="java">                                      <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dcountthresh</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<td class="new_line diff-line-num" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

987

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<pre style="margin: 0;"> <span id="LC987" class="line" lang="java">                                      <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numsplitbins</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

857

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<td class="new_line diff-line-num old" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC857" class="line" lang="java">                                      <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bstacked</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

988

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<pre style="margin: 0;">+<span id="LC988" class="line" lang="java">                                      <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bsplitcols</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nnummarksplit</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmarksplitindex</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bstacked</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bmixed</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

858

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<td class="new_line diff-line-num" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

989

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<pre style="margin: 0;"> <span id="LC989" class="line" lang="java">                                            <span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

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<td class="new_line diff-line-num" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

990

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<pre style="margin: 0;"> <span id="LC990" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

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<td class="new_line diff-line-num" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC991" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -879,13 +1010,13 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

879

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<td class="new_line diff-line-num" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1010

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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

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<td class="new_line diff-line-num" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1011

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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="java">                <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"empty line found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szchromlengthfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

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<td class="new_line diff-line-num" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

882

</td>

<td class="new_line diff-line-num old" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC882" class="line" lang="java">     <span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1013

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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="java">            <span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim();</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

<td class="new_line diff-line-num" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1014" class="line" lang="java">            <span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">],</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

<td class="new_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1015" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

<td class="new_line diff-line-num" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1016" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

</td>

<td class="new_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1017" class="line" lang="java">                <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"missing chromosome length for "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">allines</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szchromlengthfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

</td>

<td class="new_line diff-line-num" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1018" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

888

</td>

<td class="new_line diff-line-num old" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC888" class="line" lang="java">     <span class="n" style="color: #333;">lengths</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1019

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1019" class="line" lang="java">            <span class="n" style="color: #333;">lengths</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

<td class="new_line diff-line-num" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1020

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1020" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

</td>

<td class="new_line diff-line-num" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1021

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1021" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

</td>

<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1022" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -967,7 +1098,12 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

967

</td>

<td class="new_line diff-line-num" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="java">                  <span class="n" style="color: #333;">alfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

968

</td>

<td class="new_line diff-line-num" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1099" class="line" lang="java">                  <span class="n" style="color: #333;">hmfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmark</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

969

</td>

<td class="new_line diff-line-num" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1100

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1100" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

970

</td>

<td class="new_line diff-line-num old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC970" class="line" lang="java">        <span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1101

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1101" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1102

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1102" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1103

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1103" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1104

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1104" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">//added in v1.23 to only count once a given file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1105

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1105" class="line" lang="java">                  <span class="n" style="color: #333;">alfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1106

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1106" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

971

</td>

<td class="new_line diff-line-num" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1107

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1107" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

</td>

<td class="new_line diff-line-num" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1108

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1108" class="line" lang="java">            <span class="n" style="color: #333;">ncellmarkentry</span><span class="o" style="font-weight: 600;">++;</span>          </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

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<td class="new_line diff-line-num" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1050,7 +1186,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

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<td class="new_line diff-line-num" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1186

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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

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<td class="new_line diff-line-num" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1187

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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//loading data for the cell type</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

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<td class="new_line diff-line-num" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1188

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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="java">            <span class="n" style="color: #333;">loadGrid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grid</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpresentmarks</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">marks</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nshift</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1053

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<td class="new_line diff-line-num old" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1053" class="line" lang="java">                     <span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmfiles</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1189

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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="java">                     <span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmfiles</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szmarkdir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">bmixed</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

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<td class="new_line diff-line-num" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bcontrolfile</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1055

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<td class="new_line diff-line-num" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1191

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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1056

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<td class="new_line diff-line-num" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1192

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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">gridcontrol</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)||(</span><span class="n" style="color: #333;">gridcontrol</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">numcontrolmarks</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1066,7 +1202,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1066

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<td class="new_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1067

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<td class="new_line diff-line-num" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="java">               <span class="c1" style="color: #998; font-style: italic;">//we have control data loading cell type data for that</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1068

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<td class="new_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="java">               <span class="n" style="color: #333;">loadGrid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gridcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpresentcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpresentmarkscontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">marks</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nshift</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bcenterinterval</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1069

</td>

<td class="new_line diff-line-num old" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1069" class="line" lang="java">                        <span class="n" style="color: #333;">hmfilescontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcontroldir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">npseudocountcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1205

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1205" class="line" lang="java">                        <span class="n" style="color: #333;">hmfilescontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcontroldir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hmchrom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">npseudocountcontrol</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpeaks</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bbinarizebam</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bpairend</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">bmixed</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1070

</td>

<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1206" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1071

</td>

<td class="new_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1207

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1207" class="line" lang="java">            </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1072

</td>

<td class="new_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1208" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2566,7 +2702,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2566

</td>

<td class="new_line diff-line-num" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2702

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<pre style="margin: 0;"> <span id="LC2702" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcontrolDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">allfilescontrol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" header line must have two columns delimited by a tab found only one in "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2567

</td>

<td class="new_line diff-line-num" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2703

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2703" class="line" lang="java">                                                      <span class="n" style="color: #333;">szheader</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2568

</td>

<td class="new_line diff-line-num" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2704

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2704" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2569

</td>

<td class="new_line diff-line-num old" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2569" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2705

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2705" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2570

</td>

<td class="new_line diff-line-num" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2706

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2706" class="line" lang="java">               <span class="n" style="color: #333;">hmcontrol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szkey</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">allfilescontrol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2571

</td>

<td class="new_line diff-line-num" data-linenumber="2707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2707

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2707" class="line" lang="java">               <span class="n" style="color: #333;">brcontrol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="2572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2572

</td>

<td class="new_line diff-line-num" data-linenumber="2708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2708

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2708" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2588,7 +2724,7 @@ public class Preprocessing</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2588

</td>

<td class="new_line diff-line-num" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2724

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2724" class="line" lang="java">               <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">signalchromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" is empty!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2589

</td>

<td class="new_line diff-line-num" data-linenumber="2725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2725

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2725" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2590

</td>

<td class="new_line diff-line-num" data-linenumber="2726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2726

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2726" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2591

</td>

<td class="new_line diff-line-num old" data-linenumber="2727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2591" class="line" lang="java">           <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2727

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2727" class="line" lang="java">           <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2592

</td>

<td class="new_line diff-line-num" data-linenumber="2728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2728

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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="java">           <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2593

</td>

<td class="new_line diff-line-num" data-linenumber="2729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2729

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2729" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2594

</td>

<td class="new_line diff-line-num" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2730

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<pre style="margin: 0;"> <span id="LC2730" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">al</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcellsToIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrcell</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2641,7 +2777,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2641

</td>

<td class="new_line diff-line-num" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2777

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<pre style="margin: 0;"> <span id="LC2777" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Only found one entry for line "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szHeaderLine1</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szbinneddataDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfilename</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2642

</td>

<td class="new_line diff-line-num" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2778

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<pre style="margin: 0;"> <span id="LC2778" class="line" lang="java">                                                      <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" expecting 2"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2643

</td>

<td class="new_line diff-line-num" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2779

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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2644

</td>

<td class="new_line diff-line-num old" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2644" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2780

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2780" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2645

</td>

<td class="new_line diff-line-num" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2781

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2781" class="line" lang="java">               <span class="n" style="color: #333;">chroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2646

</td>

<td class="new_line diff-line-num" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2782

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2782" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcontrolfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcontrol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2647

</td>

<td class="new_line diff-line-num" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2783

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2783" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcontrolfilename</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2714,7 +2850,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2714

</td>

<td class="new_line diff-line-num" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2850

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2850" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2715

</td>

<td class="new_line diff-line-num" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2851

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<pre style="margin: 0;"> <span id="LC2851" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">grid_nchrom_nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grid_nchrom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2716

</td>

<td class="new_line diff-line-num" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2852

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2852" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">gridcontrol_nchrom_nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gridcontrol_nchrom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nbin</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2717

</td>

<td class="new_line diff-line-num old" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2717" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2853

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2853" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left"> </span>"</span><span class="o" style="font-weight: 600;">);</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//updated in 1.23</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2718

</td>

<td class="new_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2854

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2854" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2719

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<td class="new_line diff-line-num" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2855

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<pre style="margin: 0;"> <span id="LC2855" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2720

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<td class="new_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2856

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<pre style="margin: 0;"> <span id="LC2856" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfilename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" did not find the expected "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" marks in this line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2731,7 +2867,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2731

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<td class="new_line diff-line-num" data-linenumber="2867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2867

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2867" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"The number of lines in the control file "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2732

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<td class="new_line diff-line-num" data-linenumber="2868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2868

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2868" class="line" lang="java">                             <span class="n" style="color: #333;">szcontrolDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfilename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not match that in the signal file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szbinneddataDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcontrolfilename</span><span class="o" style="font-weight: 600;">);</span> </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2733

</td>

<td class="new_line diff-line-num" data-linenumber="2869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2869

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2869" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2734

</td>

<td class="new_line diff-line-num old" data-linenumber="2870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2734" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineControl</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2870

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2870" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineControl</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2735

</td>

<td class="new_line diff-line-num" data-linenumber="2871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2871

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2871" class="line" lang="java">                  <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nmark</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarkscontrol</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nmark</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2736

</td>

<td class="new_line diff-line-num" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2872

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2872" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2737

</td>

<td class="new_line diff-line-num" data-linenumber="2873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2873

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<pre style="margin: 0;"> <span id="LC2873" class="line" lang="java">                      <span class="c1" style="color: #998; font-style: italic;">//reading in the control data</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3186,7 +3322,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3186

</td>

<td class="new_line diff-line-num" data-linenumber="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3322

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<pre style="margin: 0;"> <span id="LC3322" class="line" lang="java">               <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szbinneddataDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">signalchromfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" does not contain any data!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3187

</td>

<td class="new_line diff-line-num" data-linenumber="3323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3323

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<pre style="margin: 0;"> <span id="LC3323" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3188

</td>

<td class="new_line diff-line-num" data-linenumber="3324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3324

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<pre style="margin: 0;"> <span id="LC3324" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3189

</td>

<td class="new_line diff-line-num old" data-linenumber="3325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3189" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3325

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3325" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3190

</td>

<td class="new_line diff-line-num" data-linenumber="3326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3326

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<pre style="margin: 0;"> <span id="LC3326" class="line" lang="java">           <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3191

</td>

<td class="new_line diff-line-num" data-linenumber="3327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3327

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3327" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3192

</td>

<td class="new_line diff-line-num" data-linenumber="3328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3328

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<pre style="margin: 0;"> <span id="LC3328" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">al</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcellsToIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrcell</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3241,7 +3377,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3241

</td>

<td class="new_line diff-line-num" data-linenumber="3377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3377

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3377" class="line" lang="java">               <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3242

</td>

<td class="new_line diff-line-num" data-linenumber="3378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3378

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<pre style="margin: 0;"> <span id="LC3378" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3243

</td>

<td class="new_line diff-line-num" data-linenumber="3379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3379

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<pre style="margin: 0;"> <span id="LC3379" class="line" lang="java">                  <span class="n" style="color: #333;">ntotallocs</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3244

</td>

<td class="new_line diff-line-num old" data-linenumber="3380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3244" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3380

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3380" class="line" lang="java">                  <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3245

</td>

<td class="new_line diff-line-num" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3381

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3381" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3246

</td>

<td class="new_line diff-line-num" data-linenumber="3382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3382

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3382" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3247

</td>

<td class="new_line diff-line-num" data-linenumber="3383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3383

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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfilename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" did not find the expected "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" marks in this line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3249,7 +3385,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3249

</td>

<td class="new_line diff-line-num" data-linenumber="3385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3385

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3385" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3250

</td>

<td class="new_line diff-line-num" data-linenumber="3386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3386

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<pre style="margin: 0;"> <span id="LC3386" class="line" lang="java">                  <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3251

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<td class="new_line diff-line-num" data-linenumber="3387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3387

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3387" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3252

</td>

<td class="new_line diff-line-num old" data-linenumber="3388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3252" class="line" lang="java">                      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span>  <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span>                   </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3388

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3388" class="line" lang="java">                      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span>  <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span>                </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3253

</td>

<td class="new_line diff-line-num" data-linenumber="3389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3389

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3389" class="line" lang="java">                      <span class="n" style="color: #333;">sumtags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dval</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3254

</td>

<td class="new_line diff-line-num" data-linenumber="3390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3390

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3390" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3255

</td>

<td class="new_line diff-line-num" data-linenumber="3391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3391

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3391" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3314,8 +3450,8 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3314

</td>

<td class="new_line diff-line-num" data-linenumber="3450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3450

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3450" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3315

</td>

<td class="new_line diff-line-num" data-linenumber="3451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3451

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3451" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3316

</td>

<td class="new_line diff-line-num" data-linenumber="3452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3452

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3452" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nsplit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3317

</td>

<td class="new_line diff-line-num old" data-linenumber="3453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3317" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3318

</td>

<td class="new_line diff-line-num old" data-linenumber="3453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3318" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="3453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3453" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3454" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3455" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bopen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3456

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<pre style="margin: 0;"> <span id="LC3456" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">GZIPOutputStream</span> <span class="n" style="color: #333;">pwzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3321

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<td class="new_line diff-line-num" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3457" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3339,12 +3475,12 @@ public class Preprocessing</td>

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<pre style="margin: 0;"> <span id="LC3475" class="line" lang="java">                           <span class="n" style="color: #333;">bopen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3340

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<td class="new_line diff-line-num" data-linenumber="3476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3476" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

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3341

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<td class="new_line diff-line-num" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3477

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<pre style="margin: 0;"> <span id="LC3477" class="line" lang="java">                      </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3342" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3478" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3343

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<td class="new_line diff-line-num" data-linenumber="3479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3479

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<pre style="margin: 0;"> <span id="LC3479" class="line" lang="java">                        <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sbout</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3344

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<td class="new_line diff-line-num" data-linenumber="3480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3480

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<pre style="margin: 0;"> <span id="LC3480" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3345

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<td class="new_line diff-line-num" data-linenumber="3481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3481

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<pre style="margin: 0;"> <span id="LC3481" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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3346

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<td class="new_line diff-line-num" data-linenumber="3482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3482

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<pre style="margin: 0;"> <span id="LC3482" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3347" class="line" lang="java">                <span class="idiff left right">        </span>   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3483" class="line" lang="java">                <span class="idiff left">       </span>   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim());</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3348

</td>

<td class="new_line diff-line-num" data-linenumber="3484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3484

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3484" class="line" lang="java">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3349

</td>

<td class="new_line diff-line-num" data-linenumber="3485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3485

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3485" class="line" lang="java">                           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3350

</td>

<td class="new_line diff-line-num" data-linenumber="3486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3486

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3486" class="line" lang="java">                              <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3362,7 +3498,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3362

</td>

<td class="new_line diff-line-num" data-linenumber="3498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3498

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3498" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3363

</td>

<td class="new_line diff-line-num" data-linenumber="3499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3499

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3499" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3364

</td>

<td class="new_line diff-line-num" data-linenumber="3500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3500

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3500" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3365

</td>

<td class="new_line diff-line-num old" data-linenumber="3501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3365" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3501

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3501" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3366

</td>

<td class="new_line diff-line-num" data-linenumber="3502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3502

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3502" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3367

</td>

<td class="new_line diff-line-num" data-linenumber="3503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3503

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3503" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3368

</td>

<td class="new_line diff-line-num" data-linenumber="3504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3504

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3504" class="line" lang="java">                           <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\n"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3400,7 +3536,7 @@ public class Preprocessing</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3400

</td>

<td class="new_line diff-line-num" data-linenumber="3536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3536

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3536" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3401

</td>

<td class="new_line diff-line-num" data-linenumber="3537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3537

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3537" class="line" lang="java">                  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3402

</td>

<td class="new_line diff-line-num" data-linenumber="3538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3538

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3538" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3403

</td>

<td class="new_line diff-line-num old" data-linenumber="3539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3403" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szoutputDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"_binary.txt.gz"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="3539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3539" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szoutputDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>+</span><span class="s" style="color: #d14;">"_binary.txt.gz"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3404

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<td class="new_line diff-line-num" data-linenumber="3540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3540" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3405

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<td class="new_line diff-line-num" data-linenumber="3541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3541

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<pre style="margin: 0;"> <span id="LC3541" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">GZIPOutputStream</span> <span class="n" style="color: #333;">pwzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">GZIPOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">FileOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3542" class="line" lang="java">                     <span class="c1" style="color: #998; font-style: italic;">//PrintWriter pw = new PrintWriter(new FileWriter(szfile));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3415,12 +3551,12 @@ public class Preprocessing</td>

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<pre style="margin: 0;"> <span id="LC3551" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3552" class="line" lang="java">                     <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="3417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3553" class="line" lang="java">                     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3418" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3554" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3555

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<pre style="margin: 0;"> <span id="LC3555" class="line" lang="java">                        <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sbout</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3420

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<td class="new_line diff-line-num" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3556

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<pre style="margin: 0;"> <span id="LC3556" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3421

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<td class="new_line diff-line-num" data-linenumber="3557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3557

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<pre style="margin: 0;"> <span id="LC3557" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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3422

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<td class="new_line diff-line-num" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3558

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<pre style="margin: 0;"> <span id="LC3558" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3423

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<td class="new_line diff-line-num old" data-linenumber="3559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3423" class="line" lang="java">                <span class="idiff left right">       </span>    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3559

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3559" class="line" lang="java">                <span class="idiff left">       </span>    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim());</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3424

</td>

<td class="new_line diff-line-num" data-linenumber="3560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3560

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3560" class="line" lang="java">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3425

</td>

<td class="new_line diff-line-num" data-linenumber="3561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3561

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3561" class="line" lang="java">                           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3426

</td>

<td class="new_line diff-line-num" data-linenumber="3562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3562

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3562" class="line" lang="java">                              <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3438,7 +3574,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3438

</td>

<td class="new_line diff-line-num" data-linenumber="3574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3574

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3574" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3439

</td>

<td class="new_line diff-line-num" data-linenumber="3575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3575

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3575" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3440

</td>

<td class="new_line diff-line-num" data-linenumber="3576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3576

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3576" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3441

</td>

<td class="new_line diff-line-num old" data-linenumber="3577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3441" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3577

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3577" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3442

</td>

<td class="new_line diff-line-num" data-linenumber="3578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3578

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3578" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3443

</td>

<td class="new_line diff-line-num" data-linenumber="3579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3579

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3579" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3444

</td>

<td class="new_line diff-line-num" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3580

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3580" class="line" lang="java">                            <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\n"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3470,8 +3606,8 @@ public class Preprocessing</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3470

</td>

<td class="new_line diff-line-num" data-linenumber="3606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3606

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3606" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3471

</td>

<td class="new_line diff-line-num" data-linenumber="3607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3607

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3607" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3472

</td>

<td class="new_line diff-line-num" data-linenumber="3608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3608

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3608" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nsplit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3473

</td>

<td class="new_line diff-line-num old" data-linenumber="3609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3473" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3474

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<td class="new_line diff-line-num old" data-linenumber="3609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3474" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3609" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3610

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<pre style="margin: 0;">+<span id="LC3610" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3475

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<td class="new_line diff-line-num" data-linenumber="3611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3611

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<pre style="margin: 0;"> <span id="LC3611" class="line" lang="java">                     <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bopen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3476

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<td class="new_line diff-line-num" data-linenumber="3612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3612

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<pre style="margin: 0;"> <span id="LC3612" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3477

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<td class="new_line diff-line-num" data-linenumber="3613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3613

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<pre style="margin: 0;"> <span id="LC3613" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3489,10 +3625,10 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3489

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<td class="new_line diff-line-num" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3625

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<pre style="margin: 0;"> <span id="LC3625" class="line" lang="java">                            <span class="n" style="color: #333;">bopen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3490

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<td class="new_line diff-line-num" data-linenumber="3626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3626

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<pre style="margin: 0;"> <span id="LC3626" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3491

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<td class="new_line diff-line-num" data-linenumber="3627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3627

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3627" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3492

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<td class="new_line diff-line-num old" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3492" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3628

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<pre style="margin: 0;">+<span id="LC3628" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3493

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<td class="new_line diff-line-num" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3629

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<pre style="margin: 0;"> <span id="LC3629" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3494

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<td class="new_line diff-line-num" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3630

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<pre style="margin: 0;"> <span id="LC3630" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3495

</td>

<td class="new_line diff-line-num old" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3495" class="line" lang="java">                <span class="idiff left right">       </span>    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3631

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<pre style="margin: 0;">+<span id="LC3631" class="line" lang="java">                <span class="idiff left">       </span>    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim());</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3496

</td>

<td class="new_line diff-line-num" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3632

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3632" class="line" lang="java">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3497

</td>

<td class="new_line diff-line-num" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3633

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3633" class="line" lang="java">                           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3498

</td>

<td class="new_line diff-line-num" data-linenumber="3634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3634

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3634" class="line" lang="java">                              <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3507,7 +3643,7 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3507

</td>

<td class="new_line diff-line-num" data-linenumber="3643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3643

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3643" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3508

</td>

<td class="new_line diff-line-num" data-linenumber="3644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3644

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3644" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3509

</td>

<td class="new_line diff-line-num" data-linenumber="3645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3645

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3645" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3510

</td>

<td class="new_line diff-line-num old" data-linenumber="3646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3510" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3646

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3646" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3511

</td>

<td class="new_line diff-line-num" data-linenumber="3647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3647

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3647" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3512

</td>

<td class="new_line diff-line-num" data-linenumber="3648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3648

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3648" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3513

</td>

<td class="new_line diff-line-num" data-linenumber="3649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3649

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3649" class="line" lang="java">                           <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3538,7 +3674,7 @@ public class Preprocessing</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3538

</td>

<td class="new_line diff-line-num" data-linenumber="3674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3674

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3674" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3539

</td>

<td class="new_line diff-line-num" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3675

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3675" class="line" lang="java">                  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3540

</td>

<td class="new_line diff-line-num" data-linenumber="3676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3676

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3676" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3541

</td>

<td class="new_line diff-line-num old" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3541" class="line" lang="java">        <span class="idiff left right">        </span>     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szoutputDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"_binary.txt"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3677

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3677" class="line" lang="java">        <span class="idiff left">       </span>     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szoutputDIR</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span>+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>+</span><span class="s" style="color: #d14;">"_binary.txt"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3542

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<td class="new_line diff-line-num" data-linenumber="3678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3678

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<pre style="margin: 0;"> <span id="LC3678" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3543

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<td class="new_line diff-line-num" data-linenumber="3679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3679

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<pre style="margin: 0;"> <span id="LC3679" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3544

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<td class="new_line diff-line-num" data-linenumber="3680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3680

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<pre style="margin: 0;"> <span id="LC3680" class="line" lang="java">                     <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szChromCellLine</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3546,10 +3682,10 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3546

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<pre style="margin: 0;"> <span id="LC3682" class="line" lang="java">                     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3547

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<td class="new_line diff-line-num" data-linenumber="3683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3683" class="line" lang="java">                     <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3548

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<td class="new_line diff-line-num" data-linenumber="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3684

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<pre style="margin: 0;"> <span id="LC3684" class="line" lang="java">                     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3549

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<td class="new_line diff-line-num old" data-linenumber="3685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3549" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3685

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<pre style="margin: 0;">+<span id="LC3685" class="line" lang="java">                        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3550

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<td class="new_line diff-line-num" data-linenumber="3686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3686

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<pre style="margin: 0;"> <span id="LC3686" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nummarks</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3551

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<td class="new_line diff-line-num" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3687

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<pre style="margin: 0;"> <span id="LC3687" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3552

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<td class="new_line diff-line-num old" data-linenumber="3688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3552" class="line" lang="java">                <span class="idiff left right">        </span>   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3688

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<pre style="margin: 0;">+<span id="LC3688" class="line" lang="java">                <span class="idiff left">       </span>   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//.trim());</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3553

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<td class="new_line diff-line-num" data-linenumber="3689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3689" class="line" lang="java">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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3554

</td>

<td class="new_line diff-line-num" data-linenumber="3690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3690

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3690" class="line" lang="java">                           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3555

</td>

<td class="new_line diff-line-num" data-linenumber="3691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3691

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3691" class="line" lang="java">                              <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3564,7 +3700,7 @@ public class Preprocessing</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3564

</td>

<td class="new_line diff-line-num" data-linenumber="3700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3700

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3700" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3565

</td>

<td class="new_line diff-line-num" data-linenumber="3701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3701

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3701" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3566

</td>

<td class="new_line diff-line-num" data-linenumber="3702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3702

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3702" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3567

</td>

<td class="new_line diff-line-num old" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3567" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3703

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3703" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//.trim());</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3568

</td>

<td class="new_line diff-line-num" data-linenumber="3704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3704

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3704" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3569

</td>

<td class="new_line diff-line-num" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3705

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3705" class="line" lang="java">                        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3570

</td>

<td class="new_line diff-line-num" data-linenumber="3706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3706

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3706" class="line" lang="java">                           <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"2"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3671,7 +3807,10 @@ public class Preprocessing</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3671

</td>

<td class="new_line diff-line-num" data-linenumber="3807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3807

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3807" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">//added hidden check in v.1.11</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3672

</td>

<td class="new_line diff-line-num" data-linenumber="3808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3808

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3808" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//read first two lines</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3673

</td>

<td class="new_line diff-line-num" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3809

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3809" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//maps the first line to the buffered reader</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3674

</td>

<td class="new_line diff-line-num old" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3674" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">brfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrpath</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3810

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3810" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//updating in v1.23 so not so many open files at once</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3811

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3811" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szpathfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szcurrpath</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3812

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3812" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//BufferedReader brfile = Util.getBufferedReader(szcurrpath+"/"+szcurrfile);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3813

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3813" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">brfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szpathfile</span><span class="o" style="font-weight: 600;">);</span><span class="c1" style="color: #998; font-style: italic;">//szcurrpath+"/"+szcurrfile);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3675

</td>

<td class="new_line diff-line-num" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3814

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3814" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szheader1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3676

</td>

<td class="new_line diff-line-num" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3815

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3815" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader1</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3677

</td>

<td class="new_line diff-line-num" data-linenumber="3816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3816

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3816" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3684,6 +3823,7 @@ public class Preprocessing</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3684

</td>

<td class="new_line diff-line-num" data-linenumber="3823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3823

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3823" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3685

</td>

<td class="new_line diff-line-num" data-linenumber="3824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3824

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3824" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3686

</td>

<td class="new_line diff-line-num" data-linenumber="3825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3825

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3825" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szheader2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3826

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3826" class="line" lang="java">                  <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3687

</td>

<td class="new_line diff-line-num" data-linenumber="3827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3827

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3827" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3688

</td>

<td class="new_line diff-line-num" data-linenumber="3828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3828

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3828" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader2A</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3689

</td>

<td class="new_line diff-line-num" data-linenumber="3829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3829

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3829" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3693,7 +3833,7 @@ public class Preprocessing</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3693

</td>

<td class="new_line diff-line-num" data-linenumber="3833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3833

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3833" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3694

</td>

<td class="new_line diff-line-num" data-linenumber="3834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3834

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3834" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Inconsistent header lines in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcurrpath</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" found "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szheader2</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" and "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szheader2A</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3695

</td>

<td class="new_line diff-line-num" data-linenumber="3835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3835

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3835" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3696

</td>

<td class="new_line diff-line-num old" data-linenumber="3836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3696" class="line" lang="java">                  <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">brfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3836

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<pre style="margin: 0;">+<span id="LC3836" class="line" lang="java">                  <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">szpathfile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">);</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>brfile);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3697

</td>

<td class="new_line diff-line-num" data-linenumber="3837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3837

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3837" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3698

</td>

<td class="new_line diff-line-num" data-linenumber="3838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3838

</td>

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<pre style="margin: 0;"> <span id="LC3838" class="line" lang="java">                  <span class="n" style="color: #333;">hsfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3699

</td>

<td class="new_line diff-line-num" data-linenumber="3839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3839

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3839" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3711,10 +3851,29 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3711

</td>

<td class="new_line diff-line-num" data-linenumber="3851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3851

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<pre style="margin: 0;"> <span id="LC3851" class="line" lang="java">       <span class="c1" style="color: #998; font-style: italic;">//sbmergedheader.append(szheader2A[0]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3712

</td>

<td class="new_line diff-line-num" data-linenumber="3852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3852

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<pre style="margin: 0;"> <span id="LC3852" class="line" lang="java">       <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">notpresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">szheader2A</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3713

</td>

<td class="new_line diff-line-num" data-linenumber="3853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3853

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3853" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3854

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<pre style="margin: 0;">+<span id="LC3854" class="line" lang="java">       <span class="c1" style="color: #998; font-style: italic;">//added in v1.23 to only count mark once</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3855

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3855" class="line" lang="java">       <span class="nc" style="color: #458; font-weight: 600;">HashSet</span> <span class="n" style="color: #333;">hsmarkpresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashSet</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3856

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3856" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3714

</td>

<td class="new_line diff-line-num" data-linenumber="3857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3857

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3857" class="line" lang="java">       <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">szheader2A</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3715

</td>

<td class="new_line diff-line-num" data-linenumber="3858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3858

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3858" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3716

</td>

<td class="new_line diff-line-num" data-linenumber="3859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3859

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3859" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szheader2A</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">],</span> <span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3717

</td>

<td class="new_line diff-line-num" data-linenumber="3860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3860

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3860" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ntokens</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3861

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3861" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3862

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3862" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//added in v1.23 to only count mark once</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3863

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3863" class="line" lang="java">           <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3864

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3864" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3865

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3865" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szmarktoken</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3866

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3866" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hsmarkpresent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szmarktoken</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3867

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3867" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3868

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3868" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Feature "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmarktoken</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is not unique. Found in multiple files being merged"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3869

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3869" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3870

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<pre style="margin: 0;">+<span id="LC3870" class="line" lang="java">              <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3871

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<pre style="margin: 0;">+<span id="LC3871" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3872

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3872" class="line" lang="java">                  <span class="n" style="color: #333;">hsmarkpresent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szmarktoken</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3873

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3873" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3874

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3874" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3875

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3875" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3876

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3876" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3718

</td>

<td class="new_line diff-line-num" data-linenumber="3877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3877

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3877" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sbnotpresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3719

</td>

<td class="new_line diff-line-num" data-linenumber="3878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3878

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3878" class="line" lang="java">           <span class="n" style="color: #333;">sbnotpresent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3720

</td>

<td class="new_line diff-line-num" data-linenumber="3879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3879

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3879" class="line" lang="java">           <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">na</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">na</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ntokens</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">na</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3756,8 +3915,10 @@ public class Preprocessing</td>

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3756

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<td class="new_line diff-line-num" data-linenumber="3915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3915

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<pre style="margin: 0;"> <span id="LC3915" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chromfilescombine</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3757

</td>

<td class="new_line diff-line-num" data-linenumber="3916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3916

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<pre style="margin: 0;"> <span id="LC3916" class="line" lang="java">           <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">subdirall</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3758

</td>

<td class="new_line diff-line-num" data-linenumber="3917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3917

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<pre style="margin: 0;"> <span id="LC3917" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3759

</td>

<td class="new_line diff-line-num old" data-linenumber="3918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3759" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">br</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3760

</td>

<td class="new_line diff-line-num old" data-linenumber="3918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3760" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">br</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3918

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<pre style="margin: 0;">+<span id="LC3918" class="line" lang="java">               <span class="c1" style="color: #998; font-style: italic;">//BufferedReader br = (BufferedReader) hmbrA[ndir].get(szcurrfile);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3919

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<pre style="margin: 0;">+<span id="LC3919" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szpathfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3920

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<pre style="margin: 0;">+<span id="LC3920" class="line" lang="java">              <span class="c1" style="color: #998; font-style: italic;">//if (br == null)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3921

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3921" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szpathfile</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3761

</td>

<td class="new_line diff-line-num" data-linenumber="3922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3922

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3922" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3762

</td>

<td class="new_line diff-line-num" data-linenumber="3923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3923

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3923" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Warning directory "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szinputdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subdirall</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" does not contain file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" going to treat as not present"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3763

</td>

<td class="new_line diff-line-num" data-linenumber="3924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3924

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3924" class="line" lang="java">                  <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3766,14 +3927,16 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="3766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3766

</td>

<td class="new_line diff-line-num" data-linenumber="3927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3927

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3927" class="line" lang="java">              <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3767

</td>

<td class="new_line diff-line-num" data-linenumber="3928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3928

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3928" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3768

</td>

<td class="new_line diff-line-num" data-linenumber="3929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3929

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3929" class="line" lang="java">                  <span class="n" style="color: #333;">bpresent</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3769

</td>

<td class="new_line diff-line-num old" data-linenumber="3930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3769" class="line" lang="java">                  <span class="n" style="color: #333;">brfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3930

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3930" class="line" lang="java">                  <span class="n" style="color: #333;">brfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szpathfile</span><span class="o" style="font-weight: 600;">);</span><span class="c1" style="color: #998; font-style: italic;">//br;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3931

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3931" class="line" lang="java">                  <span class="n" style="color: #333;">brfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3932

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3932" class="line" lang="java">                  <span class="n" style="color: #333;">brfiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3770

</td>

<td class="new_line diff-line-num" data-linenumber="3933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3933

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3933" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3771

</td>

<td class="new_line diff-line-num" data-linenumber="3934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3934

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3934" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3772

</td>

<td class="new_line diff-line-num" data-linenumber="3935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3935

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3935" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3773

</td>

<td class="new_line diff-line-num" data-linenumber="3936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3936

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3936" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3774

</td>

<td class="new_line diff-line-num" data-linenumber="3937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3937

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<pre style="margin: 0;"> <span id="LC3937" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chromfilescombine</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">],</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3775

</td>

<td class="new_line diff-line-num old" data-linenumber="3938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3775" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3776

</td>

<td class="new_line diff-line-num old" data-linenumber="3938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC3776" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3938

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3938" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3939

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3939" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3777

</td>

<td class="new_line diff-line-num" data-linenumber="3940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3940

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3940" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3778

</td>

<td class="new_line diff-line-num" data-linenumber="3941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3941" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3779

</td>

<td class="new_line diff-line-num" data-linenumber="3942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3942

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3942" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bsplit</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4038,12 +4201,24 @@ public class Preprocessing</td>

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<td class="old_line diff-line-num" data-linenumber="4038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4038

</td>

<td class="new_line diff-line-num" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4201

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4201" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4039

</td>

<td class="new_line diff-line-num" data-linenumber="4202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4202

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4202" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="4040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4040

</td>

<td class="new_line diff-line-num" data-linenumber="4203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4203

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4203" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="4041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4041

</td>

<td class="new_line diff-line-num old" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4041" class="line" lang="java">           <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4204

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4204" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4205

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4205" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4206

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4206" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//  for (int ndir = 0; ndir < hmbrA.length; ndir++)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4207

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4207" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4208

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4208" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//    BufferedReader br = (BufferedReader) hmbrA[ndir].get(szcurrfile);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4209

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4209" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//    if (br != null)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4210

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4210" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//    {</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4211

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4211" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//       br.close();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4212

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4212" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//    }</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4213

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4213" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4214

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4214" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4215

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4215" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4216

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4216" class="line" lang="java">           <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">brfiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="4042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4042

</td>

<td class="new_line diff-line-num" data-linenumber="4217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4217

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4217" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="4043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4043

</td>

<td class="new_line diff-line-num old" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4043" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">br</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrfile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="4044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4044

</td>

<td class="new_line diff-line-num old" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC4044" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">br</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="4045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4218

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4218" class="line" lang="java">               <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>BufferedReader br = (BufferedReader) hmbrA[ndir].get(szcurrfile);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4219

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4219" class="line" lang="java">               <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">br<span class="idiff left">files</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ndir</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4045

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<td class="new_line diff-line-num" data-linenumber="4220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4220

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4220" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4046

</td>

<td class="new_line diff-line-num old" data-linenumber="4221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4046" class="line" lang="java">                  <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4221

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4221" class="line" lang="java">                  <span class="n" style="color: #333;">br<span class="idiff left">files</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ndir</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4047

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<td class="new_line diff-line-num" data-linenumber="4222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4222

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<pre style="margin: 0;"> <span id="LC4222" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4048

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<td class="new_line diff-line-num" data-linenumber="4223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4223

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<pre style="margin: 0;"> <span id="LC4223" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4049

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<td class="new_line diff-line-num" data-linenumber="4224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4224

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4224" class="line" lang="java"></span>

</pre>

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<br>

</li>

<li id="4fb31ca7c49b2c49cfd549091ba94777db11f494">

<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/74464e34f6ac40bf5985f89e2ddf6b9dfebcc3e0...48f250d34bb651f4bee1dde863e84925132b42b1#4fb31ca7c49b2c49cfd549091ba94777db11f494"><strong>edu/mit/compbio/ChromHMM/StateAnalysis.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -248,6 +248,11 @@ public class StateAnalysis</td>

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248

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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="java">       <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nactualindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="java">       <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nnonhiddencount</span><span class="o" style="font-weight: 600;">];</span><span class="c1" style="color: #998; font-style: italic;">// dir.list(); </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java">       <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nnonhiddencount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC252" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java">          <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No files found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC254" class="line" lang="java">       <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC255" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="java">              <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="java">       <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">])).</span><span class="na" style="color: #008080;">isHidden</span><span class="o" style="font-weight: 600;">())</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,7 +312,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szHeader</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java">             <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szposteriordir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szposteriorfiles_nfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is empty!"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szHeader</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((!</span><span class="n" style="color: #333;">szcurrcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">))&&(!</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)))</span></span>

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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java">             <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,7 +320,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span></span>

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<td class="new_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="java">            <span class="n" style="color: #333;">bposteriorfound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numlines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java">            <span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -327,7 +332,7 @@ public class StateAnalysis</td>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numcurrstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="java">               <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="java">               <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="java">               <span class="n" style="color: #333;">bfirst</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="java">               <span class="n" style="color: #333;">nfirstindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="java">               <span class="n" style="color: #333;">numposteriorstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numcurrstates</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -360,7 +365,7 @@ public class StateAnalysis</td>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="java">               <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">posterior_nline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">posterior</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nline</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="java">                      <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numposteriorstates</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="java">                      <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseFloat</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseFloat</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="java">                  <span class="n" style="color: #333;">posterior_nline</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fval</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="java">                  <span class="n" style="color: #333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fval</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -381,13 +386,13 @@ public class StateAnalysis</td>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="java">               <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//gets the start and end coordinates</span></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="java">                  <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="java">                  <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="java">                  <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java">                  <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java">                  <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java">                  <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="java"></span>

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388

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

390

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<td class="new_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="java">                     <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="java">                     <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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391

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

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397

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

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398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -695,9 +700,9 @@ public class StateAnalysis</td>

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="java">        <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span> </span>

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<td class="old_line diff-line-num" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

698

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<td class="new_line diff-line-num old" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC698" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

699

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<td class="new_line diff-line-num old" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC699" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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700

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<pre style="margin: 0;">-<span id="LC700" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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703

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC703" class="line" lang="java">     <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC704" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

701

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<td class="new_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nbinsize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

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<td class="new_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="java">     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="java">         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with coordinates in input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". -b binsize should match parameter value to LearnModel or "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -705,7 +710,7 @@ public class StateAnalysis</td>

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705

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<td class="new_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

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<td class="new_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegincoord</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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707

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712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcoord</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

708

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<td class="new_line diff-line-num old" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="java">     <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="java">     <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC714" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<td class="new_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="java">     <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

</td>

<td class="new_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC716" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -783,7 +788,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<pre style="margin: 0;"> <span id="LC788" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC789" class="line" lang="java">           <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

<td class="new_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC790" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

786

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<td class="new_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC786" class="line" lang="java">              <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="java">              <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

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<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

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<pre style="margin: 0;"> <span id="LC792" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<pre style="margin: 0;"> <span id="LC793" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<td class="new_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC794" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -872,6 +877,11 @@ public class StateAnalysis</td>

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC878" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nactualindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

874

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<td class="new_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC879" class="line" lang="java">        <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nnonhiddencount</span><span class="o" style="font-weight: 600;">];</span><span class="c1" style="color: #998; font-style: italic;">// dir.list(); </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC880" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nnonhiddencount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

881

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<pre style="margin: 0;">+<span id="LC881" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

882

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<pre style="margin: 0;">+<span id="LC882" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No files found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

883

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<pre style="margin: 0;">+<span id="LC883" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC884" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="java">               <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

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<pre style="margin: 0;"> <span id="LC886" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">])).</span><span class="na" style="color: #008080;">isHidden</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -925,13 +935,13 @@ public class StateAnalysis</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC935" class="line" lang="java">     <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span>  <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

</td>

<td class="new_line diff-line-num" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC936" class="line" lang="java">     <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

927

</td>

<td class="new_line diff-line-num" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC937" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

928

</td>

<td class="new_line diff-line-num old" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC928" class="line" lang="java">        <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

929

</td>

<td class="new_line diff-line-num old" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC929" class="line" lang="java">        <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

930

</td>

<td class="new_line diff-line-num old" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC930" class="line" lang="java">        <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

938

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC938" class="line" lang="java">        <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

939

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC939" class="line" lang="java">        <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

940

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC940" class="line" lang="java">        <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

</td>

<td class="new_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC941" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

</td>

<td class="new_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC942" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

933

</td>

<td class="new_line diff-line-num" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC943" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

934

</td>

<td class="new_line diff-line-num old" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC934" class="line" lang="java">            <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

944

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC944" class="line" lang="java">            <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

<td class="new_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC945" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

</td>

<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC946" class="line" lang="java">     <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

947

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC947" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1244,6 +1254,11 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1244

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<td class="new_line diff-line-num" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1254

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1254" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1245

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<td class="new_line diff-line-num" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1255

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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nactualindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1246

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<td class="new_line diff-line-num" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1256

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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="java">             <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nnonhiddencount</span><span class="o" style="font-weight: 600;">];</span><span class="c1" style="color: #998; font-style: italic;">// dir.list(); </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1257

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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="java">             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nnonhiddencount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1258

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1258" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1259

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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="java">                <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No files found in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1260

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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1261

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1261" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1247

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<td class="new_line diff-line-num" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1262

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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="java">             <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1248

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<td class="new_line diff-line-num" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1263

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1263" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1249

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<td class="new_line diff-line-num" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1264

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1264" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filesWithHidden</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">])).</span><span class="na" style="color: #008080;">isHidden</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1309,9 +1324,9 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1309

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<td class="new_line diff-line-num" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1324

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1324" class="line" lang="java">             <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1310

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<td class="new_line diff-line-num" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1325

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1325" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1311

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<td class="new_line diff-line-num" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1326

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1326" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1312

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<td class="new_line diff-line-num old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1312" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1313" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1314

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<td class="new_line diff-line-num old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1327

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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1329

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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1315

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<td class="new_line diff-line-num" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1330

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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nbinsize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1316

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<td class="new_line diff-line-num" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1331

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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1317

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<td class="new_line diff-line-num" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1332

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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="java">                <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with coordinates in input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". -b binsize should match parameter value to LearnModel or "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1319,7 +1334,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1319

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<td class="new_line diff-line-num" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1334

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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1320

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<td class="new_line diff-line-num" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1335

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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//int nbegin = nbegincoord/nbinsize;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1321

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<td class="new_line diff-line-num" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1336

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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcoord</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1322

</td>

<td class="new_line diff-line-num old" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1322" class="line" lang="java">          <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1337

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1337" class="line" lang="java">          <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1323

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<td class="new_line diff-line-num" data-linenumber="1338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1338

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1338" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1324

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<td class="new_line diff-line-num" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1339

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1339" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1325

</td>

<td class="new_line diff-line-num" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1340

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1340" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1398,7 +1413,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1398

</td>

<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1413

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1413" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1399

</td>

<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1414

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1414" class="line" lang="java">                <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1400

</td>

<td class="new_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1415

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1415" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1401

</td>

<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1401" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1416

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1416" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1402

</td>

<td class="new_line diff-line-num" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1417

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1417" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1403

</td>

<td class="new_line diff-line-num" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1418

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1418" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1404

</td>

<td class="new_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1419

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1419" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1461,12 +1476,12 @@ public class StateAnalysis</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1461

</td>

<td class="new_line diff-line-num" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1476

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1476" class="line" lang="java">                <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1462

</td>

<td class="new_line diff-line-num" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1477

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1477" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1463

</td>

<td class="new_line diff-line-num" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1478

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1478" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1464

</td>

<td class="new_line diff-line-num old" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1464" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1479

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1479" class="line" lang="java">             <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1465

</td>

<td class="new_line diff-line-num" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1480

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1480" class="line" lang="java">             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchromwant</span><span class="o" style="font-weight: 600;">))</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1466

</td>

<td class="new_line diff-line-num" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1481

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1481" class="line" lang="java">                <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1467

</td>

<td class="new_line diff-line-num" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1482

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1482" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1468

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<td class="new_line diff-line-num old" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1468" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1469

</td>

<td class="new_line diff-line-num old" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1469" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1483

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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1484

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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1470

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<td class="new_line diff-line-num" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1485

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1485" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1471

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<td class="new_line diff-line-num" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1486

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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="java">             <span class="c1" style="color: #998; font-style: italic;">//if (nbegincoord % nbinsize != 0)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1472

</td>

<td class="new_line diff-line-num" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1487

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<pre style="margin: 0;"> <span id="LC1487" class="line" lang="java">             <span class="c1" style="color: #998; font-style: italic;">// {</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1474,7 +1489,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1474

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<td class="new_line diff-line-num" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1489

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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="java">             <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1475

</td>

<td class="new_line diff-line-num" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1490

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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegincoord</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1476

</td>

<td class="new_line diff-line-num" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1491

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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcoord</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1477

</td>

<td class="new_line diff-line-num old" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1477" class="line" lang="java">             <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1492

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1492" class="line" lang="java">             <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1478

</td>

<td class="new_line diff-line-num" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1493

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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="java">             <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1479

</td>

<td class="new_line diff-line-num" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1494

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1494" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1480

</td>

<td class="new_line diff-line-num" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1495

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1495" class="line" lang="java">             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1528,7 +1543,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

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<td class="new_line diff-line-num" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1543

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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

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<td class="new_line diff-line-num" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1544

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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="java">                   <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1530

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<td class="new_line diff-line-num" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1531

</td>

<td class="new_line diff-line-num old" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1531" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1546

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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="java">                      <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1532

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<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1533

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<td class="new_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

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<td class="new_line diff-line-num" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1549

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<pre style="margin: 0;"> <span id="LC1549" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1571,13 +1586,13 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1571

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<td class="new_line diff-line-num" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1586

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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="java">             <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span>  <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1572

</td>

<td class="new_line diff-line-num" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1587

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1587" class="line" lang="java">             <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1573

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<td class="new_line diff-line-num" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1588

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1588" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1574

</td>

<td class="new_line diff-line-num old" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1574" class="line" lang="java">                <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1575

</td>

<td class="new_line diff-line-num old" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1575" class="line" lang="java">                <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1576

</td>

<td class="new_line diff-line-num old" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1576" class="line" lang="java">                <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1589

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1589" class="line" lang="java">                <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1590

</td>

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<pre style="margin: 0;">+<span id="LC1590" class="line" lang="java">                <span class="n" style="color: #333;">nstartindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1591

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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="java">                <span class="n" style="color: #333;">nendindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1577

</td>

<td class="new_line diff-line-num" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1592

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1592" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1578

</td>

<td class="new_line diff-line-num" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1593

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<pre style="margin: 0;"> <span id="LC1593" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1579

</td>

<td class="new_line diff-line-num" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1594

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1594" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1580

</td>

<td class="new_line diff-line-num old" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1580" class="line" lang="java">                   <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1595

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1595" class="line" lang="java">                   <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1581

</td>

<td class="new_line diff-line-num" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1596

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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1582

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<td class="new_line diff-line-num" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1597

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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1583

</td>

<td class="new_line diff-line-num" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1598

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1598" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1854,8 +1869,8 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1854

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<td class="new_line diff-line-num" data-linenumber="1869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1869

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<pre style="margin: 0;"> <span id="LC1869" class="line" lang="java">           <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1855

</td>

<td class="new_line diff-line-num" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1870

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1870" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1856

</td>

<td class="new_line diff-line-num" data-linenumber="1871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1871

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1871" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1857

</td>

<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1857" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1858

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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1858" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1872" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1873

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1873" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1859

</td>

<td class="new_line diff-line-num" data-linenumber="1874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1874

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1874" class="line" lang="java">              <span class="n" style="color: #333;">hmlabelExtend</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szID</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szLabelExtend</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1860

</td>

<td class="new_line diff-line-num" data-linenumber="1875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1875

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1875" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1861

</td>

<td class="new_line diff-line-num" data-linenumber="1876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1876

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1876" class="line" lang="java">           <span class="n" style="color: #333;">bridlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1888,6 +1903,11 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1888

</td>

<td class="new_line diff-line-num" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1903

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1903" class="line" lang="java">        <span class="n" style="color: #333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setGroupingUsed</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1889

</td>

<td class="new_line diff-line-num" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1904

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1904" class="line" lang="java">        <span class="n" style="color: #333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setMinimumFractionDigits</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1890

</td>

<td class="new_line diff-line-num" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1905

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1905" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1906

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1906" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">NumberFormat</span> <span class="n" style="color: #333;">nf10</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">NumberFormat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1907

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1907" class="line" lang="java">        <span class="n" style="color: #333;">nf10</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setMaximumFractionDigits</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1908

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1908" class="line" lang="java">        <span class="n" style="color: #333;">nf10</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setGroupingUsed</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1909

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1909" class="line" lang="java">        <span class="n" style="color: #333;">nf10</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setMinimumFractionDigits</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1910

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1910" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1891

</td>

<td class="new_line diff-line-num" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1911

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1911" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".txt"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1892

</td>

<td class="new_line diff-line-num" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1912" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".txt"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1893

</td>

<td class="new_line diff-line-num" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1913" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1963,7 +1983,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1963

</td>

<td class="new_line diff-line-num" data-linenumber="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1983

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1983" class="line" lang="java">        <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Base\t100"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1964

</td>

<td class="new_line diff-line-num" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1984

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1984" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1965

</td>

<td class="new_line diff-line-num" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1985

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1985" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1966

</td>

<td class="new_line diff-line-num old" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1966" class="line" lang="java">            <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nf<span class="idiff left right">5</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333;">dsumlabel</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1986

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1986" class="line" lang="java">            <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nf<span class="idiff left right">10</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333;">dsumlabel</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1967

</td>

<td class="new_line diff-line-num" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1987

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1987" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1968

</td>

<td class="new_line diff-line-num" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1988

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1988" class="line" lang="java">        <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1969

</td>

<td class="new_line diff-line-num" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1989

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1989" class="line" lang="java">        <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2134,10 +2154,10 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2134

</td>

<td class="new_line diff-line-num" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2154

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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2135

</td>

<td class="new_line diff-line-num" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2155

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2155" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2136

</td>

<td class="new_line diff-line-num" data-linenumber="2156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2156

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2156" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2137

</td>

<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2137" class="line" lang="java">               <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2138

</td>

<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2138" class="line" lang="java">               <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2139

</td>

<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2139" class="line" lang="java">               <span class="n" style="color: #333;">nstrandindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2140

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<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2140" class="line" lang="java">               <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2157

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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="java">               <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2158

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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="java">               <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2159

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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="java">               <span class="n" style="color: #333;">nstrandindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2160

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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="java">               <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2141

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<td class="new_line diff-line-num" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2161

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<pre style="margin: 0;"> <span id="LC2161" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2142

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<td class="new_line diff-line-num" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2162

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<pre style="margin: 0;"> <span id="LC2162" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2143

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<td class="new_line diff-line-num" data-linenumber="2163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2163

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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="java">        <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2145,9 +2165,9 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2145

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<td class="new_line diff-line-num" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2165

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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2146

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<td class="new_line diff-line-num" data-linenumber="2166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2166

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<pre style="margin: 0;"> <span id="LC2166" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2147

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<td class="new_line diff-line-num" data-linenumber="2167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2167

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2167" class="line" lang="java">               <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2148

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<td class="new_line diff-line-num old" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2148" class="line" lang="java">               <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2149

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<td class="new_line diff-line-num old" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2149" class="line" lang="java">               <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2150

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<td class="new_line diff-line-num old" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2150" class="line" lang="java">               <span class="n" style="color: #333;">nstrandindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2168

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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="java">               <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2169

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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="java">               <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2170

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<pre style="margin: 0;">+<span id="LC2170" class="line" lang="java">               <span class="n" style="color: #333;">nstrandindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2151

</td>

<td class="new_line diff-line-num" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2171

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<pre style="margin: 0;"> <span id="LC2171" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2152

</td>

<td class="new_line diff-line-num" data-linenumber="2172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2172

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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2153

</td>

<td class="new_line diff-line-num" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2173

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<pre style="margin: 0;"> <span id="LC2173" class="line" lang="java">        <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2155,9 +2175,9 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2155

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<td class="new_line diff-line-num" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2175

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<pre style="margin: 0;"> <span id="LC2175" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2156

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<td class="new_line diff-line-num" data-linenumber="2176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2176

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<pre style="margin: 0;"> <span id="LC2176" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2157

</td>

<td class="new_line diff-line-num" data-linenumber="2177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2177

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2177" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2158

</td>

<td class="new_line diff-line-num old" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2158" class="line" lang="java">              <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2159

</td>

<td class="new_line diff-line-num old" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2159" class="line" lang="java">              <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2160

</td>

<td class="new_line diff-line-num old" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2160" class="line" lang="java">              <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2178

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2178" class="line" lang="java">              <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2179

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2179" class="line" lang="java">              <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2180

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<pre style="margin: 0;">+<span id="LC2180" class="line" lang="java">              <span class="n" style="color: #333;">nsignalindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2161

</td>

<td class="new_line diff-line-num" data-linenumber="2181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2181

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<pre style="margin: 0;"> <span id="LC2181" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2162

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<td class="new_line diff-line-num" data-linenumber="2182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2182

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<pre style="margin: 0;"> <span id="LC2182" class="line" lang="java">           <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//if (szcolfields == null)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2163

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<td class="new_line diff-line-num" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2183

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<pre style="margin: 0;"> <span id="LC2183" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2169,8 +2189,8 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2169

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<td class="new_line diff-line-num" data-linenumber="2189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2189

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<pre style="margin: 0;"> <span id="LC2189" class="line" lang="java">           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2170

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<td class="new_line diff-line-num" data-linenumber="2190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2190

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<pre style="margin: 0;"> <span id="LC2190" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2171

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<td class="new_line diff-line-num" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2191

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<pre style="margin: 0;"> <span id="LC2191" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolfields</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2172

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<td class="new_line diff-line-num old" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2172" class="line" lang="java">              <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2173

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<td class="new_line diff-line-num old" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2173" class="line" lang="java">              <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2192

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2192" class="line" lang="java">              <span class="n" style="color: #333;">nchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2193

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2193" class="line" lang="java">              <span class="n" style="color: #333;">npositionindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolfields</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2174

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<td class="new_line diff-line-num" data-linenumber="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2194

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2194" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2175

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<td class="new_line diff-line-num" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2195

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2195" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2176

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<td class="new_line diff-line-num" data-linenumber="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2196

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2196" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2211,6 +2231,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2211

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<td class="new_line diff-line-num" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2231

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2231" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2212

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2232

</td>

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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2213

</td>

<td class="new_line diff-line-num" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2233

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2233" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2234

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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span>  <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2214

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<td class="new_line diff-line-num" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2235

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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//an array of chromosome names</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2215

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<td class="new_line diff-line-num" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2236

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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alchromindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2216

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<td class="new_line diff-line-num" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2237

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2237" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2247,13 +2268,13 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2247

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<td class="new_line diff-line-num" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2268

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<pre style="margin: 0;"> <span id="LC2268" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2248

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<td class="new_line diff-line-num" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2269

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<pre style="margin: 0;"> <span id="LC2269" class="line" lang="java">               <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2249

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<td class="new_line diff-line-num" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2270

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<pre style="margin: 0;"> <span id="LC2270" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2250

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<td class="new_line diff-line-num old" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2250" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2271

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2271" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2251

</td>

<td class="new_line diff-line-num" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2272

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2272" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//assumes segments are in standard bed format which to get to </span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2252

</td>

<td class="new_line diff-line-num" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2273

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2273" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//0-based inclusive requires substract 1 from the end</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2253

</td>

<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2253" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//int nbegin = Integer.parseInt(st.nextToken())/nbinsize; </span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2254

</td>

<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2254" class="line" lang="java">            <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2255

</td>

<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2255" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2256

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<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2256" class="line" lang="java">            <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2274

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<pre style="margin: 0;">+<span id="LC2274" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//int nbegin = Integer.parseInt(st.nextToken()<span class="idiff left right">.trim()</span>)/nbinsize; </span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2275

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<pre style="margin: 0;">+<span id="LC2275" class="line" lang="java">            <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2276

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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2277

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<pre style="margin: 0;">+<span id="LC2277" class="line" lang="java">            <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2257

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<td class="new_line diff-line-num" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2278

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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2258

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<td class="new_line diff-line-num" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2279

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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2259

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<td class="new_line diff-line-num" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2280

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<pre style="margin: 0;"> <span id="LC2280" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2326,7 +2347,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2326

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<td class="new_line diff-line-num" data-linenumber="2347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2347

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<pre style="margin: 0;"> <span id="LC2347" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2327

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<td class="new_line diff-line-num" data-linenumber="2348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2348

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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="java">                  <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2328

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<td class="new_line diff-line-num" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2349

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<pre style="margin: 0;"> <span id="LC2349" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2329

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<td class="new_line diff-line-num old" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2329" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2350

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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2330

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<td class="new_line diff-line-num" data-linenumber="2351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2351

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<pre style="margin: 0;"> <span id="LC2351" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2331

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<td class="new_line diff-line-num" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2352

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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2332

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<td class="new_line diff-line-num" data-linenumber="2353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2353

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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="java">            </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2403,14 +2424,16 @@ public class StateAnalysis</td>

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2403

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<td class="new_line diff-line-num" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2424

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2424" class="line" lang="java">                 <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2404

</td>

<td class="new_line diff-line-num" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2425

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2425" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2405

</td>

<td class="new_line diff-line-num" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2426

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2426" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2406

</td>

<td class="new_line diff-line-num old" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2406" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2427

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2427" class="line" lang="java">              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2407

</td>

<td class="new_line diff-line-num" data-linenumber="2428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2428

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2428" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">szchromwant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2408

</td>

<td class="new_line diff-line-num" data-linenumber="2429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2429

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2429" class="line" lang="java">                  <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2430

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2430" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2431

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2431" class="line" lang="java">              <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2409

</td>

<td class="new_line diff-line-num" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2432

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2432" class="line" lang="java">              <span class="c1" style="color: #998; font-style: italic;">//assumes segments are in standard bed format which to get to </span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2410

</td>

<td class="new_line diff-line-num" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2433

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2433" class="line" lang="java">              <span class="c1" style="color: #998; font-style: italic;">//0-based inclusive requires substract 1 from the end</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2411

</td>

<td class="new_line diff-line-num old" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2411" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2412

</td>

<td class="new_line diff-line-num old" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2412" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2413

</td>

<td class="new_line diff-line-num old" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2413" class="line" lang="java">              <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2434

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2434" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2435

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2435" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2436

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2436" class="line" lang="java">              <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2414

</td>

<td class="new_line diff-line-num" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2437

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2437" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2415

</td>

<td class="new_line diff-line-num" data-linenumber="2438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2438

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2438" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2416

</td>

<td class="new_line diff-line-num" data-linenumber="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2439

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2439" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2464,7 +2487,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2464

</td>

<td class="new_line diff-line-num" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2487

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2487" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2465

</td>

<td class="new_line diff-line-num" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2488

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2488" class="line" lang="java">                    <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2466

</td>

<td class="new_line diff-line-num" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2489

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2489" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2467

</td>

<td class="new_line diff-line-num old" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2467" class="line" lang="java">                       <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2490

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2490" class="line" lang="java">                       <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2468

</td>

<td class="new_line diff-line-num" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2491

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2491" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2469

</td>

<td class="new_line diff-line-num" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2492

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2492" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2470

</td>

<td class="new_line diff-line-num" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2493

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2493" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2575,6 +2598,12 @@ public class StateAnalysis</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2575

</td>

<td class="new_line diff-line-num" data-linenumber="2598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2598

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2598" class="line" lang="java">           <span class="n" style="color: #333;">brcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span>          </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2576

</td>

<td class="new_line diff-line-num" data-linenumber="2599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2599

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2599" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2577

</td>

<td class="new_line diff-line-num" data-linenumber="2600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2600

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2600" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2601

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2601" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">bchrommatch</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2602

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2602" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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</td>

<td class="new_line diff-line-num new" data-linenumber="2603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2603

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<pre style="margin: 0;">+<span id="LC2603" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No chromosome name matches found between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2604

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<pre style="margin: 0;">+<span id="LC2604" class="line" lang="java">                                               <span class="s" style="color: #d14;">" and those in the segmentation file."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2605

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<pre style="margin: 0;">+<span id="LC2605" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2606

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2606" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2578

</td>

<td class="new_line diff-line-num" data-linenumber="2607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2607

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<pre style="margin: 0;"> <span id="LC2607" class="line" lang="java">        <span class="n" style="color: #333;">outputneighborhood</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nspacing</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numright</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2579

</td>

<td class="new_line diff-line-num" data-linenumber="2608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2608

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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="java">                           <span class="n" style="color: #333;">numleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)),</span><span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2580

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<td class="new_line diff-line-num" data-linenumber="2609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2609

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<pre style="margin: 0;"> <span id="LC2609" class="line" lang="java">                           <span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2610,6 +2639,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2610

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<td class="new_line diff-line-num" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2639

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<pre style="margin: 0;"> <span id="LC2639" class="line" lang="java">                                        <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span>  <span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2611

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<td class="new_line diff-line-num" data-linenumber="2640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2640

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<pre style="margin: 0;"> <span id="LC2640" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2612

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<td class="new_line diff-line-num" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2641

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<pre style="margin: 0;"> <span id="LC2641" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//highmem</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2642

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<pre style="margin: 0;">+<span id="LC2642" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span>  <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2613

</td>

<td class="new_line diff-line-num" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2643

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<pre style="margin: 0;"> <span id="LC2643" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//stores all the segments in the data</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2614

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<td class="new_line diff-line-num" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2644

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<pre style="margin: 0;"> <span id="LC2644" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alsegments</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2615

</td>

<td class="new_line diff-line-num" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2645

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2645" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2645,12 +2675,12 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2645

</td>

<td class="new_line diff-line-num" data-linenumber="2675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2675

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<pre style="margin: 0;"> <span id="LC2675" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2646

</td>

<td class="new_line diff-line-num" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2676

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<pre style="margin: 0;"> <span id="LC2676" class="line" lang="java">                <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2647

</td>

<td class="new_line diff-line-num" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2677

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<pre style="margin: 0;"> <span id="LC2677" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2648

</td>

<td class="new_line diff-line-num old" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2648" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2678

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2678" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2649

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<td class="new_line diff-line-num" data-linenumber="2679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2679

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<pre style="margin: 0;"> <span id="LC2679" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//assumes segments are in standard bed format which to get to </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2650

</td>

<td class="new_line diff-line-num" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2680

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<pre style="margin: 0;"> <span id="LC2680" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//0-based inclusive requires substract 1 from the end</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2651

</td>

<td class="new_line diff-line-num old" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2651" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2652

</td>

<td class="new_line diff-line-num old" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2652" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2653

</td>

<td class="new_line diff-line-num old" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2653" class="line" lang="java">            <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2681

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2681" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2682

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2682" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span> </span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2683

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2683" class="line" lang="java">            <span class="n" style="color: #333;">szlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2654

</td>

<td class="new_line diff-line-num" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2684

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2684" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">slabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2655

</td>

<td class="new_line diff-line-num" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2685

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2685" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2656

</td>

<td class="new_line diff-line-num" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2686

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2686" class="line" lang="java">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2728,7 +2758,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2728

</td>

<td class="new_line diff-line-num" data-linenumber="2758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2758

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2758" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2729

</td>

<td class="new_line diff-line-num" data-linenumber="2759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2759

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2759" class="line" lang="java">                  <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">ex2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2730

</td>

<td class="new_line diff-line-num" data-linenumber="2760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2760

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2760" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2731

</td>

<td class="new_line diff-line-num old" data-linenumber="2761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2731" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID <span class="idiff left right">file </span>found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2761

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2761" class="line" lang="java">                     <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"In fourth column neither state number or ID found in segmentation file. Use '-labels' option to run overlap enrichment treating fourth column as labels"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2732

</td>

<td class="new_line diff-line-num" data-linenumber="2762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2762

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2762" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2733

</td>

<td class="new_line diff-line-num" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2763

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2763" class="line" lang="java">               <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2734

</td>

<td class="new_line diff-line-num" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2764

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2764" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2854,6 +2884,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2854

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<td class="new_line diff-line-num" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2884

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2884" class="line" lang="java">           <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2855

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<td class="new_line diff-line-num" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2885

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2885" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">objChrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2856

</td>

<td class="new_line diff-line-num" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2886

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2886" class="line" lang="java">              <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">labels_nchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2887

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2887" class="line" lang="java">              <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2857

</td>

<td class="new_line diff-line-num" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2888

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2888" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2858

</td>

<td class="new_line diff-line-num" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2889

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2889" class="line" lang="java">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bposstrand</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2859

</td>

<td class="new_line diff-line-num" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2890

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2890" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2887,6 +2918,13 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2887

</td>

<td class="new_line diff-line-num" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2918

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2918" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2888

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<td class="new_line diff-line-num" data-linenumber="2919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2919

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2919" class="line" lang="java">        <span class="n" style="color: #333;">brcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span>             </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2889

</td>

<td class="new_line diff-line-num" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2920" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2921

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2921" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2922

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2922" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">bchrommatch</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2923

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2923" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2924

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2924" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No chromosome name matches found between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2925

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2925" class="line" lang="java">                                               <span class="s" style="color: #d14;">" and those in the segmentation file."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2926

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2926" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2927

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2927" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2890

</td>

<td class="new_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2928

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<pre style="margin: 0;"> <span id="LC2928" class="line" lang="java">        <span class="n" style="color: #333;">outputneighborhood</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nspacing</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numright</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2891

</td>

<td class="new_line diff-line-num" data-linenumber="2929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2929

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2929" class="line" lang="java">                           <span class="n" style="color: #333;">numleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)),</span><span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2892

</td>

<td class="new_line diff-line-num" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2930

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2930" class="line" lang="java">                           <span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2920,6 +2958,8 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

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<td class="new_line diff-line-num" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2958

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<pre style="margin: 0;"> <span id="LC2958" class="line" lang="java">                                             <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">busestrand</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">noffsetanchor</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2921

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<td class="new_line diff-line-num" data-linenumber="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2959

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<pre style="margin: 0;"> <span id="LC2959" class="line" lang="java">                                           <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2922

</td>

<td class="new_line diff-line-num" data-linenumber="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2960

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2960" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2961

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2961" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2962

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<pre style="margin: 0;">+<span id="LC2962" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span>  <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2923

</td>

<td class="new_line diff-line-num" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2963

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<pre style="margin: 0;"> <span id="LC2963" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//posterior here is really signal just using equivalent variable names</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2924

</td>

<td class="new_line diff-line-num" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2964

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<pre style="margin: 0;"> <span id="LC2964" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//list of possible posterior files</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2925

</td>

<td class="new_line diff-line-num" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

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<pre style="margin: 0;"> <span id="LC2965" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">posteriordir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szposteriordir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2959,7 +2999,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2959

</td>

<td class="new_line diff-line-num" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2999

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<pre style="margin: 0;"> <span id="LC2999" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szposteriordir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szposteriorfiles_nfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is empty!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2960

</td>

<td class="new_line diff-line-num" data-linenumber="3000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3000

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<pre style="margin: 0;"> <span id="LC3000" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2961

</td>

<td class="new_line diff-line-num" data-linenumber="3001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3001

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3001" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2962

</td>

<td class="new_line diff-line-num old" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2962" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3002

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3002" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2963

</td>

<td class="new_line diff-line-num" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3003

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3003" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((!</span><span class="n" style="color: #333;">szcurrcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">))&&(!</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2964

</td>

<td class="new_line diff-line-num" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3004

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3004" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

</td>

<td class="new_line diff-line-num" data-linenumber="3005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3005

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3005" class="line" lang="java">                    <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2970,7 +3010,7 @@ public class StateAnalysis</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2970

</td>

<td class="new_line diff-line-num" data-linenumber="3010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3010

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3010" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2971

</td>

<td class="new_line diff-line-num" data-linenumber="3011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3011

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3011" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">//must match cell type or consistent with empty cell type</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2972

</td>

<td class="new_line diff-line-num" data-linenumber="3012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3012

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3012" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2973

</td>

<td class="new_line diff-line-num old" data-linenumber="3013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2973" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3013

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<pre style="margin: 0;">+<span id="LC3013" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2974

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<td class="new_line diff-line-num" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3014

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<pre style="margin: 0;"> <span id="LC3014" class="line" lang="java">            </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2975

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<td class="new_line diff-line-num" data-linenumber="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3015

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<pre style="margin: 0;"> <span id="LC3015" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numlines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2976

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<td class="new_line diff-line-num" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3016

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<pre style="margin: 0;"> <span id="LC3016" class="line" lang="java">                   <span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span> <span class="c1" style="color: #998; font-style: italic;">//gets state header</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2982,7 +3022,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="2982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2982

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<td class="new_line diff-line-num" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3022

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<pre style="margin: 0;"> <span id="LC3022" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numcurrstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2983

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<td class="new_line diff-line-num" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3023

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<pre style="margin: 0;"> <span id="LC3023" class="line" lang="java">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2984

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<td class="new_line diff-line-num" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3024

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<pre style="margin: 0;"> <span id="LC3024" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2985

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<td class="new_line diff-line-num old" data-linenumber="3025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2985" class="line" lang="java">                       <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3025

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<pre style="margin: 0;">+<span id="LC3025" class="line" lang="java">                       <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2986

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<td class="new_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3026

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<pre style="margin: 0;"> <span id="LC3026" class="line" lang="java">                       <span class="n" style="color: #333;">bfirst</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2987

</td>

<td class="new_line diff-line-num" data-linenumber="3027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3027

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<pre style="margin: 0;"> <span id="LC3027" class="line" lang="java">                       <span class="n" style="color: #333;">nfirstindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2988

</td>

<td class="new_line diff-line-num" data-linenumber="3028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3028

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<pre style="margin: 0;"> <span id="LC3028" class="line" lang="java">                       <span class="n" style="color: #333;">numposteriorstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numcurrstates</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3036,6 +3076,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3036

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<td class="new_line diff-line-num" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3076

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3076" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3037

</td>

<td class="new_line diff-line-num" data-linenumber="3077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3077

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<pre style="margin: 0;"> <span id="LC3077" class="line" lang="java">                      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szreadchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3038

</td>

<td class="new_line diff-line-num" data-linenumber="3078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3078

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3078" class="line" lang="java">                      <span class="o" style="font-weight: 600;">{</span>  </span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3079

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<pre style="margin: 0;">+<span id="LC3079" class="line" lang="java">                         <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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3039

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<td class="new_line diff-line-num" data-linenumber="3080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3080

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<pre style="margin: 0;"> <span id="LC3080" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nanchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">npositionindex</span><span class="o" style="font-weight: 600;">])-</span><span class="n" style="color: #333;">noffsetanchor</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3040

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<td class="new_line diff-line-num" data-linenumber="3081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3081

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<pre style="margin: 0;"> <span id="LC3081" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bposstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3041

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<td class="new_line diff-line-num" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3082

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<pre style="margin: 0;"> <span id="LC3082" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busestrand</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3120,6 +3161,12 @@ public class StateAnalysis</td>

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3120

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<td class="new_line diff-line-num" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3161

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<pre style="margin: 0;"> <span id="LC3161" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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3121

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<td class="new_line diff-line-num" data-linenumber="3162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3162

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<pre style="margin: 0;"> <span id="LC3162" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No posterior file found for cell type "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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3122

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<td class="new_line diff-line-num" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3163

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<pre style="margin: 0;"> <span id="LC3163" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span>   </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3164

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<pre style="margin: 0;">+<span id="LC3164" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3165

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<pre style="margin: 0;">+<span id="LC3165" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">bchrommatch</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3166

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<pre style="margin: 0;">+<span id="LC3166" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3167

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3167" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No chromosome name matches found between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3168

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3168" class="line" lang="java">                                               <span class="s" style="color: #d14;">" and those in the segmentation file."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3169

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3169" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3123

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<td class="new_line diff-line-num" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3170

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<pre style="margin: 0;"> <span id="LC3170" class="line" lang="java"> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3124

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<td class="new_line diff-line-num" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3171

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<pre style="margin: 0;"> <span id="LC3171" class="line" lang="java">        <span class="n" style="color: #333;">outputneighborhoodsignal</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numlocs</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nspacing</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numright</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3125

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<td class="new_line diff-line-num" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3172

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<pre style="margin: 0;"> <span id="LC3172" class="line" lang="java">                                 <span class="n" style="color: #333;">numleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chorder</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szmarknames</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">chorder</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3154,6 +3201,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3154

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<td class="new_line diff-line-num" data-linenumber="3201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3201

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<pre style="margin: 0;"> <span id="LC3201" class="line" lang="java">                                              <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3155

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<td class="new_line diff-line-num" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3202

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<pre style="margin: 0;"> <span id="LC3202" class="line" lang="java">    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3156

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<td class="new_line diff-line-num" data-linenumber="3203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3203

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<pre style="margin: 0;"> <span id="LC3203" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3204

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<pre style="margin: 0;">+<span id="LC3204" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span>  <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #998; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3157

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<td class="new_line diff-line-num" data-linenumber="3205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3205

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<pre style="margin: 0;"> <span id="LC3205" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//list of possible posterior files</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3158

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<td class="new_line diff-line-num" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3206

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<pre style="margin: 0;"> <span id="LC3206" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">posteriordir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szposteriordir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3159

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<td class="new_line diff-line-num" data-linenumber="3207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3207

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<pre style="margin: 0;"> <span id="LC3207" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">posteriordir</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3191,7 +3239,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3191

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<td class="new_line diff-line-num" data-linenumber="3239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3239

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<pre style="margin: 0;"> <span id="LC3239" class="line" lang="java">                   <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szposteriordir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szposteriorfiles_nfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is empty!"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3192

</td>

<td class="new_line diff-line-num" data-linenumber="3240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3240

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<pre style="margin: 0;"> <span id="LC3240" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3193

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<td class="new_line diff-line-num" data-linenumber="3241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3241

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<pre style="margin: 0;"> <span id="LC3241" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3194

</td>

<td class="new_line diff-line-num old" data-linenumber="3242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3194" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3242

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3242" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrcell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3195

</td>

<td class="new_line diff-line-num" data-linenumber="3243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3243

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3243" class="line" lang="java">                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((!</span><span class="n" style="color: #333;">szcurrcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">))&&(!</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3196

</td>

<td class="new_line diff-line-num" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3244

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3244" class="line" lang="java">                <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3197

</td>

<td class="new_line diff-line-num" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3245

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<pre style="margin: 0;"> <span id="LC3245" class="line" lang="java">                    <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3202,7 +3250,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3202

</td>

<td class="new_line diff-line-num" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3250

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3250" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3203

</td>

<td class="new_line diff-line-num" data-linenumber="3251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3251

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<pre style="margin: 0;"> <span id="LC3251" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">//must match cell type or consistent with empty cell type</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3204

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<td class="new_line diff-line-num" data-linenumber="3252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3252

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3252" class="line" lang="java"></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3205

</td>

<td class="new_line diff-line-num old" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3205" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3253

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<pre style="margin: 0;">+<span id="LC3253" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3206

</td>

<td class="new_line diff-line-num" data-linenumber="3254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3254

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<pre style="margin: 0;"> <span id="LC3254" class="line" lang="java">            </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3207

</td>

<td class="new_line diff-line-num" data-linenumber="3255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3255

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<pre style="margin: 0;"> <span id="LC3255" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numlines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3208

</td>

<td class="new_line diff-line-num" data-linenumber="3256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3256

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<pre style="margin: 0;"> <span id="LC3256" class="line" lang="java">                   <span class="n" style="color: #333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brposterior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">();</span> <span class="c1" style="color: #998; font-style: italic;">//gets state header</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3214,7 +3262,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3214

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<td class="new_line diff-line-num" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3262

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<pre style="margin: 0;"> <span id="LC3262" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numcurrstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3215

</td>

<td class="new_line diff-line-num" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3263

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3263" class="line" lang="java">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3216

</td>

<td class="new_line diff-line-num" data-linenumber="3264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3264

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<pre style="margin: 0;"> <span id="LC3264" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3217

</td>

<td class="new_line diff-line-num old" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3217" class="line" lang="java">                       <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3265

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3265" class="line" lang="java">                       <span class="n" style="color: #333;">chorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;"><span class="idiff left">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">().</span></span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3218

</td>

<td class="new_line diff-line-num" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3266

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3266" class="line" lang="java">                       <span class="n" style="color: #333;">bfirst</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3219

</td>

<td class="new_line diff-line-num" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3267

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3267" class="line" lang="java">                       <span class="n" style="color: #333;">nfirstindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nfile</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3220

</td>

<td class="new_line diff-line-num" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3268

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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="java">                       <span class="n" style="color: #333;">numposteriorstates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numcurrstates</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3268,6 +3316,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3268

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<td class="new_line diff-line-num" data-linenumber="3316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3316

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<pre style="margin: 0;"> <span id="LC3316" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3269

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<td class="new_line diff-line-num" data-linenumber="3317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3317

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<pre style="margin: 0;"> <span id="LC3317" class="line" lang="java">                      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szreadchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3270

</td>

<td class="new_line diff-line-num" data-linenumber="3318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3318

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<pre style="margin: 0;"> <span id="LC3318" class="line" lang="java">                      <span class="o" style="font-weight: 600;">{</span>  </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3319

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3319" class="line" lang="java">                         <span class="n" style="color: #333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3271

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<td class="new_line diff-line-num" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3320

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<pre style="margin: 0;"> <span id="LC3320" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nanchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">npositionindex</span><span class="o" style="font-weight: 600;">])-</span><span class="n" style="color: #333;">noffsetanchor</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3272

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<td class="new_line diff-line-num" data-linenumber="3321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3321

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<pre style="margin: 0;"> <span id="LC3321" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bposstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3273

</td>

<td class="new_line diff-line-num" data-linenumber="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3322

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<pre style="margin: 0;"> <span id="LC3322" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">busestrand</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3350,6 +3399,12 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3350

</td>

<td class="new_line diff-line-num" data-linenumber="3399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3399

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<pre style="margin: 0;"> <span id="LC3399" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3351

</td>

<td class="new_line diff-line-num" data-linenumber="3400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3400

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<pre style="margin: 0;"> <span id="LC3400" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No posterior file found for cell type "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcell</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3352

</td>

<td class="new_line diff-line-num" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3401

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3401" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span>   </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3402

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3402" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3403

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3403" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">bchrommatch</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3404

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3404" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3405

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3405" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No chromosome name matches found between "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3406

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<pre style="margin: 0;">+<span id="LC3406" class="line" lang="java">                                               <span class="s" style="color: #d14;">" and those in the segmentation file."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3407

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3407" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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3353

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<td class="new_line diff-line-num" data-linenumber="3408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3408

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<pre style="margin: 0;"> <span id="LC3408" class="line" lang="java"> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3354

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<td class="new_line diff-line-num" data-linenumber="3409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3409

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<pre style="margin: 0;"> <span id="LC3409" class="line" lang="java">        <span class="n" style="color: #333;">outputneighborhood</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nspacing</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numright</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3355

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<td class="new_line diff-line-num" data-linenumber="3410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3410

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<pre style="margin: 0;"> <span id="LC3410" class="line" lang="java">                           <span class="n" style="color: #333;">numleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chorder</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3442,10 +3497,13 @@ public class StateAnalysis</td>

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3497

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<pre style="margin: 0;"> <span id="LC3497" class="line" lang="java">                      <span class="c1" style="color: #998; font-style: italic;">//copying over the contents</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3443

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<td class="new_line diff-line-num" data-linenumber="3498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3498

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<pre style="margin: 0;"> <span id="LC3498" class="line" lang="java">                      <span class="n" style="color: #333;">heatmapreduce</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nkeepindex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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3444

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<td class="new_line diff-line-num" data-linenumber="3499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3499

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<pre style="margin: 0;"> <span id="LC3499" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3445

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<td class="new_line diff-line-num old" data-linenumber="3500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3445" class="line" lang="java">                  <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nkeepindex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span><span class="c1" style="color: #998; font-style: italic;">//""+(nstate+1);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3500

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<pre style="margin: 0;">+<span id="LC3500" class="line" lang="java">                  <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nkeepindex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span><span class="c1" style="color: #998; font-style: italic;">//""+(nstate+1);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3446

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<td class="new_line diff-line-num" data-linenumber="3501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3501

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<pre style="margin: 0;"> <span id="LC3501" class="line" lang="java">                  <span class="n" style="color: #333;">nkeepindex</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3447

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<td class="new_line diff-line-num" data-linenumber="3502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3502

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<pre style="margin: 0;"> <span id="LC3502" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3448

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<td class="new_line diff-line-num old" data-linenumber="3503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3448" class="line" lang="java">              <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3503" class="line" lang="java">              <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//added in 1.23</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3504

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<pre style="margin: 0;">+<span id="LC3504" class="line" lang="java">              <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3505

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<pre style="margin: 0;">+<span id="LC3505" class="line" lang="java">                 <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3506" class="line" lang="java">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3449

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<td class="new_line diff-line-num" data-linenumber="3507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3507

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<pre style="margin: 0;"> <span id="LC3507" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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3450

</td>

<td class="new_line diff-line-num" data-linenumber="3508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3508

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<pre style="margin: 0;"> <span id="LC3508" class="line" lang="java">           <span class="n" style="color: #333;">heatmapfold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">heatmapreduce</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3451

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<td class="new_line diff-line-num" data-linenumber="3509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3509

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<pre style="margin: 0;"> <span id="LC3509" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3454,7 +3512,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3454

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<td class="new_line diff-line-num" data-linenumber="3512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3512

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<pre style="margin: 0;"> <span id="LC3512" class="line" lang="java">            <span class="n" style="color: #333;">rowlabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3455

</td>

<td class="new_line diff-line-num" data-linenumber="3513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3513

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<pre style="margin: 0;"> <span id="LC3513" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ni</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3456

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<td class="new_line diff-line-num" data-linenumber="3514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3514

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<pre style="margin: 0;"> <span id="LC3514" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3457

</td>

<td class="new_line diff-line-num old" data-linenumber="3515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3457" class="line" lang="java">                <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3515

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3515" class="line" lang="java">                <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3458

</td>

<td class="new_line diff-line-num" data-linenumber="3516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3516

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<pre style="margin: 0;"> <span id="LC3516" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3459

</td>

<td class="new_line diff-line-num" data-linenumber="3517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3517

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3517" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3460

</td>

<td class="new_line diff-line-num" data-linenumber="3518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3518

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3518" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3672,11 +3730,11 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3672

</td>

<td class="new_line diff-line-num" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3730

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3730" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3673

</td>

<td class="new_line diff-line-num" data-linenumber="3731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3731

</td>

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<pre style="margin: 0;"> <span id="LC3731" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//maps each mark identifier to a consistent indext value</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3674

</td>

<td class="new_line diff-line-num" data-linenumber="3732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3732

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3732" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmNameToID</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3675

</td>

<td class="new_line diff-line-num old" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3675" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szaxis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3733

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3733" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szaxis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3676

</td>

<td class="new_line diff-line-num" data-linenumber="3734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3734

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3734" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3677

</td>

<td class="new_line diff-line-num" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3735

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3735" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3678

</td>

<td class="new_line diff-line-num" data-linenumber="3736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3736

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3736" class="line" lang="java">        <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3679

</td>

<td class="new_line diff-line-num old" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3679" class="line" lang="java">            <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">(),</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3737

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3737" class="line" lang="java">            <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>,</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3680

</td>

<td class="new_line diff-line-num" data-linenumber="3738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3738

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<pre style="margin: 0;"> <span id="LC3738" class="line" lang="java">            <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3681

</td>

<td class="new_line diff-line-num" data-linenumber="3739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3739

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3739" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3682

</td>

<td class="new_line diff-line-num" data-linenumber="3740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3740

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3740" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3703,10 +3761,10 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3703

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<td class="new_line diff-line-num" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3761

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<pre style="margin: 0;"> <span id="LC3761" class="line" lang="java">                <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numstatesmain</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" lines in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szmainmodelfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" found fewer."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3704

</td>

<td class="new_line diff-line-num" data-linenumber="3762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3762

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3762" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3705

</td>

<td class="new_line diff-line-num" data-linenumber="3763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3763

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3763" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3706

</td>

<td class="new_line diff-line-num old" data-linenumber="3764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3706" class="line" lang="java">            <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3764

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3764" class="line" lang="java">            <span class="n" style="color: #333;">rowlabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3707

</td>

<td class="new_line diff-line-num" data-linenumber="3765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3765

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3765" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numcols</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3708

</td>

<td class="new_line diff-line-num" data-linenumber="3766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3766

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3766" class="line" lang="java">            <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3709

</td>

<td class="new_line diff-line-num old" data-linenumber="3767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3709" class="line" lang="java">               <span class="n" style="color: #333;">emissionparamsmain</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3767

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3767" class="line" lang="java">               <span class="n" style="color: #333;">emissionparamsmain</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3710

</td>

<td class="new_line diff-line-num" data-linenumber="3768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3768

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<pre style="margin: 0;"> <span id="LC3768" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3711

</td>

<td class="new_line diff-line-num" data-linenumber="3769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3769

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3769" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3712

</td>

<td class="new_line diff-line-num" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3770

</td>

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<pre style="margin: 0;"> <span id="LC3770" class="line" lang="java">        <span class="n" style="color: #333;">bremissions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3759,7 +3817,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3759

</td>

<td class="new_line diff-line-num" data-linenumber="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3817

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<pre style="margin: 0;"> <span id="LC3817" class="line" lang="java">                   <span class="n" style="color: #333;">ncol</span>  <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3760

</td>

<td class="new_line diff-line-num" data-linenumber="3818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3818

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<pre style="margin: 0;"> <span id="LC3818" class="line" lang="java">                   <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasMoreTokens</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3761

</td>

<td class="new_line diff-line-num" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3819

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<pre style="margin: 0;"> <span id="LC3819" class="line" lang="java">                   <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3762

</td>

<td class="new_line diff-line-num old" data-linenumber="3820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3762" class="line" lang="java">                       <span class="n" style="color: #333;">mappedcol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">())).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3820

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3820" class="line" lang="java">                       <span class="n" style="color: #333;">mappedcol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmNameToID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stheader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3763

</td>

<td class="new_line diff-line-num" data-linenumber="3821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3821

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3821" class="line" lang="java">                       <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3764

</td>

<td class="new_line diff-line-num" data-linenumber="3822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3822

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3822" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3765

</td>

<td class="new_line diff-line-num" data-linenumber="3823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3823

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3823" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3779,7 +3837,7 @@ public class StateAnalysis</td>

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<td class="old_line diff-line-num" data-linenumber="3779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3779

</td>

<td class="new_line diff-line-num" data-linenumber="3837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3837

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3837" class="line" lang="java">                    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numcols</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3780

</td>

<td class="new_line diff-line-num" data-linenumber="3838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3838

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3838" class="line" lang="java">                    <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="new_line diff-line-num" data-linenumber="3839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3839" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">//storing the emission parameter for</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3782

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<td class="new_line diff-line-num old" data-linenumber="3840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3782" class="line" lang="java">                        <span class="n" style="color: #333;">theRecEmissionFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">emissionparams</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mappedcol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3840" class="line" lang="java">                        <span class="n" style="color: #333;">theRecEmissionFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">emissionparams</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mappedcol</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">()<span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">trim</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>

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3783

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<td class="new_line diff-line-num" data-linenumber="3841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3841

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<pre style="margin: 0;"> <span id="LC3841" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="3784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3784

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<td class="new_line diff-line-num" data-linenumber="3842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3842" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="3843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3843

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<pre style="margin: 0;"> <span id="LC3843" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">//adds a record for this emission file containing the parameters, number of states, and number of marks</span></span>

</pre>

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