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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/fastqc">Debian Med / fastqc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/ca5c1101f4be4a000ddebfd0649e457b15e7936c">ca5c1101</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-17T17:24:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.11.8+dfsg'
Update to upstream version '0.11.8+dfsg'
with Debian dir bb3e97084f71f1c20831b6e2241667ffe7c622dd</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/3b97b25a6f51ad942ebc33f119689eb435153958">3b97b25a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-17T17:24:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.8+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/bac2383aae5238241b87d205bca604a0f29d56ce">bac2383a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-17T17:36:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing for 0.11.8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/9f214d8c4e7ce422cbf3912c2f583aaad6044b05">9f214d8c</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-17T17:38:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.8+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/8759cc9268ed944d4805ce2639b5fb0643bf35e4">8759cc92</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-17T17:38:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.11.8+dfsg'
Update to upstream version '0.11.8+dfsg'
with Debian dir 653883e54c5e1d263a46d769623f3cda70f7ae73</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7218c513d6f727b5ea96fc048c04738db1285799">
RELEASE_NOTES.txt
</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="#4b5bbf7edda2ae49e59c4def0bbf52a721883abd">
debian/patches/drop-fast5.patch
</a>
</li>
<li class="file-stats">
<a href="#6cdda62e4cb4e251f8a5a29f663397632907d447">
debian/patches/fastqc.patch
</a>
</li>
<li class="file-stats">
<a href="#3298ccc787ae057230815e840c980c07cee031f3">
fastqc
</a>
</li>
<li class="file-stats">
<a href="#4cd5f316a21bf415455c3026705068930e292260">
run_fastqc.bat
</a>
</li>
<li class="file-stats">
<a href="#4abecb201fc238d51df86967669e9721b0b19f86">
uk/ac/babraham/FastQC/FastQCApplication.java
</a>
</li>
<li class="file-stats">
<a href="#e9f63f51554c886d766c4f8514ac17292120173c">
uk/ac/babraham/FastQC/Graphs/LineGraph.java
</a>
</li>
<li class="file-stats">
<a href="#599886f55ff6b2afb619da338a48b076cd60db4b">
uk/ac/babraham/FastQC/Modules/DuplicationLevel.java
</a>
</li>
<li class="file-stats">
<a href="#c374db931477fae930a0a924ef5dec32c2a7cd32">
uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.java
</a>
</li>
<li class="file-stats">
<a href="#3013cb0481f38b744114f30dd2156d353af7ebf7">
uk/ac/babraham/FastQC/Results/ResultsPanel.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7218c513d6f727b5ea96fc048c04738db1285799">
<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#7218c513d6f727b5ea96fc048c04738db1285799"><strong>RELEASE_NOTES.txt</strong></a>
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<td class="diff-line-num new new_line" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">RELEASE NOTES FOR FastQC v0.11.8</span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">--------------------------------</span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">This release works around some edge cases in unusual sequence libraries</span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">and changes the behaviour of the read length module when run with the</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">--nogroup option. Other minor fixes are also present.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">RELEASE NOTES FOR FastQC v0.11.7</span>
</pre>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">--------------------------------</span>
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<td class="diff-line-num new_line" 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"></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fastqc (0.11.8+dfsg-1) unstable; urgency=medium</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 17 Oct 2018 19:25:09 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">fastqc (0.11.7+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libhtsjdk-java,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libjbzip2-java,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libcommons-math3-java</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fastqc</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fastqc.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</span>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#4b5bbf7edda2ae49e59c4def0bbf52a721883abd"><strong>debian/patches/drop-fast5.patch</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">@@ -13,8 +13,10 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> poretools, I propose to temporarily drop fast5 support from FastQC</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> to avoid a removal from testing.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/fastqc</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fastqc</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastqc/fastqc</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastqc.orig/fastqc</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastqc/fastqc</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -74,7 +74,6 @@ my $quiet;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> my $nogroup;</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> my $expgroup;</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">@@ -46,7 +48,7 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> (including being gzipped and ending with .gz) otherwise they</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> won't be grouped together correctly.</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- --nano Files come from naopore sequences and are in fast5 format. In</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- --nano Files come from na<span class="idiff left right">n</span>opore sequences and are in fast5 format. In</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- this mode you can pass in directories to process and the program</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- will take in all fast5 files within those directories and produce</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- a single output file from the sequences found in all files. </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">@@ -54,7 +56,9 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> --nofilter If running with --casava then don't remove read flagged by</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> casava as poor quality when performing the QC analysis.</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/uk/ac/babraham/FastQC/Sequence/Fast5File.java</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastqc.orig/uk/ac/babraham/FastQC/Sequence/Fast5File.java</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,107 +0,0 @@</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/**</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">@@ -164,8 +168,10 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastqc.orig/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java</span></span>
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169
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -99,9 +99,9 @@ public class SequenceFactory {</span></span>
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170
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="diff"> // We default to using all reads</span>
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171
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="diff"> return new BAMFile(file,false);</span>
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<li id="6cdda62e4cb4e251f8a5a29f663397632907d447">
<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#6cdda62e4cb4e251f8a5a29f663397632907d447"><strong>debian/patches/fastqc.patch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">From: Steffen Moeller <moeller@debian.org></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Subject: Ensure proper CLASSPATH according to location of Debian JARs</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/fastqc</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fastqc</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastqc/fastqc</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastqc.orig/fastqc</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastqc/fastqc</span></span>
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6
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -33,16 +33,15 @@ if (-e "$RealBin/uk/ac/babraham/FastQC/F</span></span>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> }</span>
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8
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); 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="38" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -36,9 +38,3 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> __DATA__</span></pre>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -405,4 +404,3 @@ BUGS</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> or in www.bioinformatics.babraham.ac.uk/bugzilla/</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff">\ No newline at end of file</span></pre>
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<li id="3298ccc787ae057230815e840c980c07cee031f3">
<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#3298ccc787ae057230815e840c980c07cee031f3"><strong>fastqc</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -327,7 +327,7 @@ DESCRIPTION</td>
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">including</span> <span class="nv" style="color: teal;">being</span> <span class="nv" style="color: teal;">gzipped</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">ending</span> <span class="nv" style="color: teal;">with</span> <span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">gz</span><span class="p">)</span> <span class="nv" style="color: teal;">otherwise</span> <span class="nv" style="color: teal;">they</span></span>
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="perl"> <span class="nv" style="color: teal;">won</span><span class="s" style="color: #d14;">'t be grouped together correctly.</span></span>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="perl"><span class="s" style="color: #d14;"> --nano Files come from naopore sequences and are in fast5 format. In</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"><span class="s" style="color: #d14;"> --nano Files come from na<span class="idiff left right">n</span>opore sequences and are in fast5 format. In</span></span>
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="perl"><span class="s" style="color: #d14;"> this mode you can pass in directories to process and the program</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="perl"><span class="s" style="color: #d14;"> will take in all fast5 files within those directories and produce</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="perl"><span class="s" style="color: #d14;"> a single output file from the sequences found in all files. </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -405,4 +405,4 @@ BUGS</td>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="perl"> <span class="nv" style="color: teal;">Any</span> <span class="nv" style="color: teal;">bugs</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">fastqc</span> <span class="nv" style="color: teal;">should</span> <span class="nv" style="color: teal;">be</span> <span class="nv" style="color: teal;">reported</span> <span class="nv" style="color: teal;">either</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">simon</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">andrews@babraham</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">uk</span></span>
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">www</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">bioinformatics</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">uk</span><span class="sr" style="color: #009926;">/bugzilla/</span></span>
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407
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="perl"> </span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="perl"> </span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="perl"> </span></pre>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#4cd5f316a21bf415455c3026705068930e292260"><strong>run_fastqc.bat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication<span class="idiff left"> %*</span></span><span class="idiff right"></span></pre>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#4abecb201fc238d51df86967669e9721b0b19f86"><strong>uk/ac/babraham/FastQC/FastQCApplication.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">@@ -54,7 +54,7 @@ import uk.ac.babraham.FastQC.Utilities.NanoporeBasename;</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastQCApplication</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">JFrame</span> <span class="o" style="font-weight: 600;">{</span> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.<span class="idiff left right">7</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.<span class="idiff left right">8</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JTabbedPane</span> <span class="n" style="color: #333;">fileTabs</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">WelcomePanel</span> <span class="n" style="color: #333;">welcomePanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#e9f63f51554c886d766c4f8514ac17292120173c"><strong>uk/ac/babraham/FastQC/Graphs/LineGraph.java</strong></a>
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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;"> * Copyright Copyright 2010-17 Simon Andrews</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;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Graphs</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.BasicStroke</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Color</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Dimension</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Graphics</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Graphics2D</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.RenderingHints</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LineGraph</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">JPanel</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">data</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Color</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">COLOURS</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">220</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="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</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="mi" style="color: #099;">220</span><span class="o" style="font-weight: 600;">),</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</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;">220</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;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">DARK_GRAY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MAGENTA</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ORANGE</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">YELLOW</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CYAN</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PINK</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">data</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;">minY</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;">maxY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</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;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</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;">graphTitle</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">data</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;">minY</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;">maxY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">maxY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xTitles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">graphTitle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">yInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findOptimalYInterval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">findOptimalYInterval</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;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</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="LC67" class="line" lang="java"> <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;">divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</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 class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">2.5</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>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC71" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tester</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC73" 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;">max</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tester</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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="n" style="color: #333;">base</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>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Dimension</span> <span class="nf" style="color: #900; font-weight: 600;">getPreferredSize</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Dimension</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <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>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Dimension</span> <span class="nf" style="color: #900; font-weight: 600;">getMinimumSize</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Dimension</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="mi" style="color: #099;">200</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">paint</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Graphics</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">paint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">);</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> </span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</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="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> </span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastY</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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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> </span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> </span>
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105
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<pre style="margin: 0;">-<span id="LC105" 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;">minY</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">yInterval</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>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">yStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">yStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yInterval</span> <span class="o" style="font-weight: 600;">*</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;">minY</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">yInterval</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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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> </span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xOffset</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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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" 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;">double</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">label</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;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">replaceAll</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 class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// Don't leave trailing .0s where we don't need them.</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">);</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" 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;">width</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">xOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">;</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> </span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">label</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;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)+(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getAscent</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>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> </span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Give the x axis a bit of breathing space</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">xOffset</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>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> </span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Draw the graph title</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">titleWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">);</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</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 class="mi" style="color: #099;">2</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;">titleWidth</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="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">);</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> </span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> </span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the axes</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Draw the xLabel under the xAxis</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</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="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabel</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;">getHeight</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>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> </span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the data points</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</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 class="n" style="color: #333;">data</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: teal;">length</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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;">baseWidth</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="LC144" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("Base Width is "+baseWidth);</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First draw faint boxes over alternating bases so you can see which is which</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Let's find the longest label, and then work out how often we can draw labels</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastXLabelEnd</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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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> </span>
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153
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<pre style="margin: 0;">-<span id="LC153" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</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: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" 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;">i</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <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;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">));</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">baseNumber</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;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseNumberWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNumber</span><span class="o" style="font-weight: 600;">);</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseNumberPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)-(</span><span class="n" style="color: #333;">baseNumberWidth</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>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> </span>
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163
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<pre style="margin: 0;">-<span id="LC163" 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;">baseNumberPosition</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastXLabelEnd</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNumber</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">baseNumberPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">);</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">lastXLabelEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseNumberPosition</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">baseNumberWidth</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>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> </span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw horizontal lines across from the y axis</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">));</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" 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;">double</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> </span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the datasets</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> </span>
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179
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<pre style="margin: 0;">-<span id="LC179" 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;">g</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setStroke</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicStroke</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>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setRenderingHint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">KEY_ANTIALIASING</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">VALUE_ANTIALIAS_ON</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> </span>
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184
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<pre style="margin: 0;">-<span id="LC184" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">]);</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> </span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</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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188
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<pre style="margin: 0;">-<span id="LC188" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">i</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;">lastY</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">thisY</span><span class="o" style="font-weight: 600;">);</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisY</span><span class="o" style="font-weight: 600;">;</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> </span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> </span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the data legend</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"></span>
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198
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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;">g</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setStroke</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicStroke</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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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setRenderingHint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">KEY_ANTIALIASING</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">VALUE_ANTIALIAS_OFF</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First we need to find the widest label</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">widestLabel</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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206
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<pre style="margin: 0;">-<span id="LC206" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">]);</span></span>
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208
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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;">width</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">widestLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">;</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java"> </span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Add 3px either side for a bit of space;</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> <span class="n" style="color: #333;">widestLabel</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First draw a box to put the legend in</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawRect</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the actual labels</span></span>
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<pre style="margin: 0;">-<span id="LC221" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">],</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">+(</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">t</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="LC224" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> </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>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getY</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;">y</span><span class="o" style="font-weight: 600;">)</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)(((</span><span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">)/(</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">))*</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java"> </span>
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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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1
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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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span><span class="idiff left right">
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span><span class="idiff left right">
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span><span class="idiff left right">
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span><span class="idiff left right">
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span><span class="idiff left right">
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span><span class="idiff left right">
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span><span class="idiff left right">
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span><span class="idiff left right">
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span><span class="idiff left right">
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span><span class="idiff left right">
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span><span class="idiff left right">
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span><span class="idiff left right">
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span><span class="idiff left right">
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Graphs</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.BasicStroke</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Color</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Dimension</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Graphics</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Graphics2D</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.RenderingHints</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LineGraph</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">JPanel</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">data</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Color</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">COLOURS</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">220</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="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</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="mi" style="color: #099;">220</span><span class="o" style="font-weight: 600;">),</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</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;">220</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;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">DARK_GRAY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MAGENTA</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ORANGE</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">YELLOW</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CYAN</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PINK</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">};</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">data</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;">minY</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;">maxY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</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;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</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;">graphTitle</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC47" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">data</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;">minY</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;">maxY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">maxY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xTitles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">graphTitle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">yInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findOptimalYInterval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> </span><span class="idiff left right">
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">findOptimalYInterval</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;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> </span><span class="idiff left right">
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</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><span class="idiff left right">
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <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;">divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</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 class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">2.5</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><span class="idiff left right">
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> </span><span class="idiff left right">
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> </span><span class="idiff left right">
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71
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<pre style="margin: 0;">+<span id="LC71" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tester</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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73
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<pre style="margin: 0;">+<span id="LC73" 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;">max</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tester</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 class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> </span><span class="idiff left right">
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="n" style="color: #333;">base</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><span class="idiff left right">
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> </span><span class="idiff left right">
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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81
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82
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> </span><span class="idiff left right">
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> </span><span class="idiff left right">
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Dimension</span> <span class="nf" style="color: #900; font-weight: 600;">getPreferredSize</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Dimension</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Dimension</span> <span class="nf" style="color: #900; font-weight: 600;">getMinimumSize</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Dimension</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">paint</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Graphics</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">paint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> </span><span class="idiff left right">
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</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="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">());</span></span><span class="idiff left right">
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> </span><span class="idiff left right">
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastY</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><span class="idiff left right">
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> </span><span class="idiff left right">
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" 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;">minY</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">yInterval</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><span class="idiff left right">
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">yStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">yStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yInterval</span> <span class="o" style="font-weight: 600;">*</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;">minY</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">yInterval</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><span class="idiff left right">
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> </span><span class="idiff left right">
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xOffset</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><span class="idiff left right">
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" 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;">double</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">label</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;">i</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">replaceAll</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 class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// Don't leave trailing .0s where we don't need them.</span></span><span class="idiff left right">
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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118
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<pre style="margin: 0;">+<span id="LC118" 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;">width</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">xOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> </span><span class="idiff left right">
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">label</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;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)+(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getAscent</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><span class="idiff left right">
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> </span><span class="idiff left right">
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Give the x axis a bit of breathing space</span></span><span class="idiff left right">
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">xOffset</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><span class="idiff left right">
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> </span><span class="idiff left right">
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Draw the graph title</span></span><span class="idiff left right">
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">titleWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphTitle</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</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 class="mi" style="color: #099;">2</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;">titleWidth</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="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> </span><span class="idiff left right">
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> </span><span class="idiff left right">
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the axes</span></span><span class="idiff left right">
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> </span><span class="idiff left right">
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Draw the xLabel under the xAxis</span></span><span class="idiff left right">
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</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="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabel</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;">getHeight</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><span class="idiff left right">
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> </span><span class="idiff left right">
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> </span><span class="idiff left right">
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the data points</span></span><span class="idiff left right">
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</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 class="n" style="color: #333;">data</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: teal;">length</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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143
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<pre style="margin: 0;">+<span id="LC143" 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;">baseWidth</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;">baseWidth</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><span class="idiff left right">
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> </span><span class="idiff left right">
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("Base Width is "+baseWidth);</span></span><span class="idiff left right">
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146
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First draw faint boxes over alternating bases so you can see which is which</span></span><span class="idiff left right">
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"> </span><span class="idiff left right">
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Let's find the longest label, and then work out how often we can draw labels</span></span><span class="idiff left right">
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> </span><span class="idiff left right">
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastXLabelEnd</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><span class="idiff left right">
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> </span><span class="idiff left right">
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153
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<pre style="margin: 0;">+<span id="LC153" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</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: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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154
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<pre style="margin: 0;">+<span id="LC154" 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;">i</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">230</span><span class="o" style="font-weight: 600;">));</span></span><span class="idiff left right">
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">baseNumber</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;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseNumberWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNumber</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseNumberPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)-(</span><span class="n" style="color: #333;">baseNumberWidth</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><span class="idiff left right">
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java"> </span><span class="idiff left right">
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163
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<pre style="margin: 0;">+<span id="LC163" 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;">baseNumberPosition</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastXLabelEnd</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNumber</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">baseNumberPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">lastXLabelEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseNumberPosition</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">baseNumberWidth</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><span class="idiff left right">
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> </span><span class="idiff left right">
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw horizontal lines across from the y axis</span></span><span class="idiff left right">
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">180</span><span class="o" style="font-weight: 600;">));</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" 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">
172
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<pre style="margin: 0;">+<span id="LC172" 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;">double</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yStart</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">yInterval</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</span></span><span class="idiff left right">
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BLACK</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> </span><span class="idiff left right">
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the datasets</span></span><span class="idiff left right">
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> </span><span class="idiff left right">
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179
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<pre style="margin: 0;">+<span id="LC179" 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;">g</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setStroke</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicStroke</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><span class="idiff left right">
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setRenderingHint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">KEY_ANTIALIASING</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">VALUE_ANTIALIAS_ON</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> </span><span class="idiff left right">
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184
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<pre style="margin: 0;">+<span id="LC184" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> </span><span class="idiff left right">
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</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><span class="idiff left right">
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188
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<pre style="margin: 0;">+<span id="LC188" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawLine</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">i</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;">lastY</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">thisY</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisY</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> </span><span class="idiff left right">
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> </span><span class="idiff left right">
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the data legend</span></span><span class="idiff left right">
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java"></span>
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198
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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;">g</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setStroke</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicStroke</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><span class="idiff left right">
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Graphics2D</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">setRenderingHint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">KEY_ANTIALIASING</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">RenderingHints</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">VALUE_ANTIALIAS_OFF</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java"> </span><span class="idiff left right">
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First we need to find the widest label</span></span><span class="idiff left right">
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">widestLabel</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><span class="idiff left right">
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206
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<pre style="margin: 0;">+<span id="LC206" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFontMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stringWidth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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208
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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;">width</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">widestLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java"> </span><span class="idiff left right">
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Add 3px either side for a bit of space;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"> <span class="n" style="color: #333;">widestLabel</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java"> </span><span class="idiff left right">
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First draw a box to put the legend in</span></span><span class="idiff left right">
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fillRect</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">));</span></span><span class="idiff left right">
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawRect</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">));</span></span><span class="idiff left right">
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java"></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the actual labels</span></span><span class="idiff left right">
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221
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<pre style="margin: 0;">+<span id="LC221" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">COLOURS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">drawString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xTitles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">],</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">getWidth</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 class="n" style="color: #333;">widestLabel</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 class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">+(</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">t</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getY</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;">y</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">40</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)(((</span><span class="n" style="color: #333;">getHeight</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">)/(</span><span class="n" style="color: #333;">maxY</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">minY</span><span class="o" style="font-weight: 600;">))*</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right"></span></pre>
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<li id="599886f55ff6b2afb619da338a48b076cd60db4b">
<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#599886f55ff6b2afb619da338a48b076cd60db4b"><strong>uk/ac/babraham/FastQC/Modules/DuplicationLevel.java</strong></a>
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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;"> * Copyright Copyright 2010-17 Simon Andrews</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;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Modules</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.DecimalFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.LineGraph</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DuplicationLevel</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">OverRepresentedSeqs</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">;</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">deduplicatedPercentages</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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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">totalPercentages</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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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxCount</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>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">percentDifferentSeqs</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="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</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>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">DecimalFormat</span> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DecimalFormat</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="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="nf" style="color: #900; font-weight: 600;">DuplicationLevel</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">OverRepresentedSeqs</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">overrepresentedModule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Plots the number of sequences which are duplicated to different levels"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC53" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC55" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC57" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC60" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC62" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> </span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calculateLevels</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> </span>
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68
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<pre style="margin: 0;">-<span id="LC68" 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;">deduplicatedPercentages</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="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> </span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">collatedCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">>();</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> </span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> </span>
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77
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<pre style="margin: 0;">-<span id="LC77" 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;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">());</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> </span>
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80
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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;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</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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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</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="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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="c1" style="color: #998; font-style: italic;">// Now we can correct each of these</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">correctedCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Double</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC94" 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;">itr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">getCorrectedCount</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">countAtUniqueLimit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">count</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("For dup level "+dupLevel+" raw count was "+count+" corrected count was "+correctedCounts.get(dupLevel));</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// From the corrected counts we can now work out the raw and deduplicated proportions</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dedupTotal</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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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rawTotal</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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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> </span>
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111
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<pre style="margin: 0;">-<span id="LC111" 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;">itc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">dedupTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">rawTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dupLevel</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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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> </span>
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120
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<pre style="margin: 0;">-<span id="LC120" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="o" style="font-weight: 600;">;</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">;</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">499</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span><span class="o" style="font-weight: 600;">;</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">99</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span><span class="o" style="font-weight: 600;">;</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">49</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</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>
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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
126
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<pre style="margin: 0;">-<span id="LC126" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">;</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">dupSlot</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">dupSlot</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">;</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> </span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("True total = "+overrepresentedModule.count+" inferred total is "+rawTotal+" dedup total is "+dedupTotal);</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> </span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;">labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" 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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">9</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;">i</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;">i</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="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
140
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<pre style="margin: 0;">-<span id="LC140" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">9</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">10"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" 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;">i</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 class="n" style="color: #333;">labels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">50"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
142
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<pre style="margin: 0;">-<span id="LC142" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">11</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">100"</span><span class="o" style="font-weight: 600;">;</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">12</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">500"</span><span class="o" style="font-weight: 600;">;</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">13</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">1k"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" 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">
145
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<pre style="margin: 0;">-<span id="LC145" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">14</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">5k"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" 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">
146
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<pre style="margin: 0;">-<span id="LC146" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">15</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">10k"</span><span class="o" style="font-weight: 600;">;</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> </span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">dedupTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">rawTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</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>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</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>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> </span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> </span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dedupTotal</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rawTotal</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>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> </span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC160" 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;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getCorrectedCount</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">totalCount</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;">duplicationLevel</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;">numberOfObservations</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> </span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("Count at limit = "+countAtLimit+" total = "+totalCount+" Dup level = "+duplicationLevel+" no obs = "+numberOfObservations);</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we can bail out early</span></span>
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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;">countAtLimit</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">;</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> </span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If there aren't enough sequences left to hide another sequence with this count then</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we can also skip the calculation</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" 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;">totalCount</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numberOfObservations</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">;</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> </span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If not then we need to see what the likelihood is that we had another sequence</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// with this number of observations which we would have missed.</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We'll start by working out the probability of NOT seeing a sequence with this duplication level</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// within the first countAtLimit sequences of numberOfObservations. This is easier than calculating</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the probability of seeing it.</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> </span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pNotSeeingAtLimit</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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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> </span>
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180
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<pre style="margin: 0;">-<span id="LC180" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">pNotSeeingAtLimit</span> <span class="o" style="font-weight: 600;">*=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)-</span><span class="n" style="color: #333;">duplicationLevel</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;">totalCount</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("At i="+i+" p is "+pNotSeeingAtLimit);</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> </span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we can invert this to get the chance of seeing a sequence with this count</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pSeeingAtLimit</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;">pNotSeeingAtLimit</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we can assume that the number we observed can be scaled up by this proportion</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">trueCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pSeeingAtLimit</span><span class="o" style="font-weight: 600;">;</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"> </span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trueCount</span><span class="o" style="font-weight: 600;">;</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">},</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence Duplication Level"</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="s" style="color: #d14;">"% Deduplicated sequences"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"% Total sequences"</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="s" style="color: #d14;">"Percent of seqs remaining if deduplicated "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">percentDifferentSeqs</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="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"duplication_levels.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Duplication level graph"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"> <span class="n" style="color: #333;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"> </span>
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209
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<pre style="margin: 0;">-<span id="LC209" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Total Deduplicated Percentage\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">percentDifferentSeqs</span><span class="o" style="font-weight: 600;">);</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" 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: teal;">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>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> </span>
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213
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<pre style="margin: 0;">-<span id="LC213" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Duplication Level\tPercentage of deduplicated\tPercentage of total\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" 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;">i</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;">i</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="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" 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: teal;">append</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;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" 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;">i</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="na" style="color: teal;">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>
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<pre style="margin: 0;">-<span id="LC217" 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: teal;">append</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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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" 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: teal;">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>
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220
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<pre style="margin: 0;">-<span id="LC220" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" 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: teal;">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>
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<pre style="margin: 0;">-<span id="LC222" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC223" 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: teal;">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>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</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="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Sequence Duplication Levels"</span><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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</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="c1" style="color: #998; font-style: italic;">// We don't need to do anything since we use </span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the data structure from the overrepresented sequences</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// module.</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC239" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Anything over 50% duplicate gets us a error</span></span>
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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;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC244" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC247" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC250" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Anything over 20% duplicate gets us a warning</span></span>
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<pre style="margin: 0;">-<span id="LC253" 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;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC255" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC258" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</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="LC262" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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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;"> * Copyright Copyright 2010-17 Simon Andrews</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;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<td class="diff-line-num new new_line" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Modules</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.DecimalFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"></span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.LineGraph</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DuplicationLevel</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">OverRepresentedSeqs</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">deduplicatedPercentages</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="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">totalPercentages</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="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxCount</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>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">percentDifferentSeqs</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="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</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>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">DecimalFormat</span> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DecimalFormat</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="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="nf" style="color: #900; font-weight: 600;">DuplicationLevel</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">OverRepresentedSeqs</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">overrepresentedModule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Plots the number of sequences which are duplicated to different levels"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> </span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calculateLevels</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> </span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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;">deduplicatedPercentages</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="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> </span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">collatedCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">>();</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> </span>
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77
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<pre style="margin: 0;">+<span id="LC77" 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;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">());</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> </span>
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80
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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;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisCount</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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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we can correct each of these</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">correctedCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Double</span><span class="o" style="font-weight: 600;">>();</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" 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;">itr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collatedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">);</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">getCorrectedCount</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">countAtUniqueLimit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">overrepresentedModule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">count</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">));</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// From the corrected counts we can now work out the raw and deduplicated proportions</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dedupTotal</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rawTotal</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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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" 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;">itc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">correctedCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="n" style="color: #333;">dedupTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">rawTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dupLevel</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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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">999</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">499</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">99</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">49</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</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>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" 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;">dupSlot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">dupSlot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">dupSlot</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">dupSlot</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dupLevel</span><span class="o" style="font-weight: 600;">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("True total = "+overrepresentedModule.count+" inferred total is "+rawTotal+" dedup total is "+dedupTotal);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="n" style="color: #333;">labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">];</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" 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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">9</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;">i</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;">i</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="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC137" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">9</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">10"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC138" 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;">i</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 class="n" style="color: #333;">labels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">50"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC139" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">11</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">100"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC140" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">12</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">500"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC141" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">13</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">1k"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC142" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">14</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">5k"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" style="width: 35px; color: rgba(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="diff-line-num new new_line" 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">
143
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<pre style="margin: 0;">+<span id="LC143" 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;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">15</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;">i</span><span class="o" style="font-weight: 600;">]=</span><span class="s" style="color: #d14;">">10k"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">dedupTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">rawTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</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>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</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>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> </span>
</pre>
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<td class="diff-line-num new new_line" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> </span>
</pre>
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<td class="diff-line-num new new_line" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dedupTotal</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rawTotal</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>
</pre>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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156
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157
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<pre style="margin: 0;">+<span id="LC157" 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;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getCorrectedCount</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">totalCount</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;">duplicationLevel</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;">numberOfObservations</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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158
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("Count at limit = "+countAtLimit+" total = "+totalCount+" Dup level = "+duplicationLevel+" no obs = "+numberOfObservations);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we can bail out early</span></span>
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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;">countAtLimit</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If there aren't enough sequences left to hide another sequence with this count then</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we can also skip the calculation</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" 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;">totalCount</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numberOfObservations</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"> </span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If not then we need to see what the likelihood is that we had another sequence</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// with this number of observations which we would have missed.</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We'll start by working out the probability of NOT seeing a sequence with this duplication level</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// within the first countAtLimit sequences of numberOfObservations. This is easier than calculating</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the probability of seeing it.</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> </span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pNotSeeingAtLimit</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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176
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177
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// To save doing long calculations which are never going to produce anything meaningful</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we'll set a limit to our p-value calculation. This is the probability below which we</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// won't increase our count by 0.01 of an observation. Once we're below this we stop caring</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// about the corrected value since it's going to be so close to the observed value that</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we can just return that instead.</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">limitOfCaring</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">/(</span><span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.01d</span><span class="o" style="font-weight: 600;">));</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">countAtLimit</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> <span class="n" style="color: #333;">pNotSeeingAtLimit</span> <span class="o" style="font-weight: 600;">*=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)-</span><span class="n" style="color: #333;">duplicationLevel</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;">totalCount</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> </span>
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188
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<pre style="margin: 0;">+<span id="LC188" 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;">pNotSeeingAtLimit</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">limitOfCaring</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="n" style="color: #333;">pNotSeeingAtLimit</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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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> </span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> </span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we can invert this to get the chance of seeing a sequence with this count</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pSeeingAtLimit</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;">pNotSeeingAtLimit</span><span class="o" style="font-weight: 600;">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we can assume that the number we observed can be scaled up by this proportion</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">trueCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numberOfObservations</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pSeeingAtLimit</span><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>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trueCount</span><span class="o" style="font-weight: 600;">;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"> </span>
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203
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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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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="java"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">},</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence Duplication Level"</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="s" style="color: #d14;">"% Deduplicated sequences"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"% Total sequences"</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="s" style="color: #d14;">"Percent of seqs remaining if deduplicated "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">percentDifferentSeqs</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="LC210" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java"> </span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"duplication_levels.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Duplication level graph"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java"> </span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java"> </span>
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219
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<pre style="margin: 0;">+<span id="LC219" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Total Deduplicated Percentage\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">percentDifferentSeqs</span><span class="o" style="font-weight: 600;">);</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" 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: teal;">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>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" 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">
223
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<pre style="margin: 0;">+<span id="LC223" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Duplication Level\tPercentage of deduplicated\tPercentage of total\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" 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;">i</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;">i</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="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" 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: teal;">append</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;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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226
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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;">i</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="na" style="color: teal;">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>
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227
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<pre style="margin: 0;">+<span id="LC227" 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: teal;">append</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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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" 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: teal;">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>
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230
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<pre style="margin: 0;">+<span id="LC230" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deduplicatedPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" 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: teal;">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>
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232
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<pre style="margin: 0;">+<span id="LC232" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalPercentages</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" 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: teal;">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>
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234
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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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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> </span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java"></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Sequence Duplication Levels"</span><span class="o" style="font-weight: 600;">;</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="java"></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We don't need to do anything since we use </span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the data structure from the overrepresented sequences</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// module.</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java"> </span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Anything over 50% duplicate gets us a error</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" 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;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="java"> </span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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257
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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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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="java"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" 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;">deduplicatedPercentages</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;">calculateLevels</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="java"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Anything over 20% duplicate gets us a warning</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" 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;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"duplication"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="java"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java"> <span class="n" style="color: #333;">deduplicatedPercentages</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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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java"> </span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#c374db931477fae930a0a924ef5dec32c2a7cd32"><strong>uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.java</strong></a>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Modules</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.LineGraph</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceLengthDistribution</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</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="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">graphCounts</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="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</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="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">calculated</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="LC38" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC41" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">},</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence Length (bp)"</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="s" style="color: #d14;">"Sequence Length"</span><span class="o" style="font-weight: 600;">},</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Distribution of sequence lengths over all sequences"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC48" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC53" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC55" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calculateDistribution</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxLen</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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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLen</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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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> </span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Find the min and max lengths</span></span>
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<pre style="margin: 0;">-<span id="LC63" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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>
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<pre style="margin: 0;">-<span id="LC65" 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;">minLen</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>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="n" style="color: #333;">minLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="n" style="color: #333;">maxLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We put one extra category either side of the actual size</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" 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;">minLen</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;">minLen</span><span class="o" style="font-weight: 600;">--;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC76" 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;">startAndInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSizeDistribution</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLen</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Work out how many categories we need</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">categories</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="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currentValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startAndInterval</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="LC81" 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;">currentValue</span><span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">categories</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="n" style="color: #333;">currentValue</span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">startAndInterval</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="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="n" style="color: #333;">graphCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</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;">categories</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">categories</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC89" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</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>
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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;">minValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startAndInterval</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;">startAndInterval</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;">i</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;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">startAndInterval</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;">startAndInterval</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;">i</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="LC93" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC94" 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;">maxValue</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> </span>
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98
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<pre style="margin: 0;">-<span id="LC98" 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;">bp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">minValue</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxValue</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" 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;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">];</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"></span>
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104
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<pre style="margin: 0;">-<span id="LC104" 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;">startAndInterval</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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;">minValue</span><span class="o" style="font-weight: 600;">;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minValue</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;">maxValue</span><span class="o" style="font-weight: 600;">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> </span>
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111
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<pre style="margin: 0;">-<span id="LC111" 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;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequence</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC119" 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;">seqLen</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;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">newLengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seqLen</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>
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<pre style="margin: 0;">-<span id="LC121" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">newLengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLengthCounts</span><span class="o" style="font-weight: 600;">;</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seqLen</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> </span>
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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>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">getSizeDistribution</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;">min</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;">max</span><span class="o" style="font-weight: 600;">)</span> <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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</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="LC134" class="line" lang="java"> </span>
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135
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<pre style="margin: 0;">-<span id="LC135" 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;">base</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> <span class="n" style="color: #333;">base</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>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">starting</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>
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<pre style="margin: 0;">-<span id="LC142" 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;">divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</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 class="mi" style="color: #099;">2</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>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="nl">OUTER:</span> <span class="k" style="font-weight: 600;">while</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> </span>
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146
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<pre style="margin: 0;">-<span id="LC146" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tester</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(((</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">)</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="n" style="color: #333;">interval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">;</span></span>
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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;">break</span> <span class="n" style="color: #333;">OUTER</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> </span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">base</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>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> </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>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we work out the first value to be plotted</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">basicDivision</span> <span class="o" style="font-weight: 600;">=</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;">min</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">testStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basicDivision</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">;</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> </span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">starting</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">testStart</span><span class="o" style="font-weight: 600;">;</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> </span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">starting</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">};</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> </span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</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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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Shows the distribution of sequence length over all sequences"</span><span class="o" style="font-weight: 600;">;</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Sequence Length Distribution"</span><span class="o" style="font-weight: 600;">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> </span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if they've turned this test off</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</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="o" style="font-weight: 600;">{</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"></span>
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192
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<pre style="margin: 0;">-<span id="LC192" 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;">lengthCounts</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if they've turned this test off</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</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="o" style="font-weight: 600;">{</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Warn if they're not all the same length</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">seenLength</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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208
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<pre style="margin: 0;">-<span id="LC208" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" 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;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="o" style="font-weight: 600;">{</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" 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;">seenLength</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC212" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java"> <span class="n" style="color: #333;">seenLength</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="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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219
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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>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java"></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"sequence_length_distribution.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence length distribution"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"> </span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="n" style="color: #333;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC227" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Length\tCount\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC228" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</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="c1" style="color: #998; font-style: italic;">// Remove any padding we added to make the graph look better</span></span>
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<pre style="margin: 0;">-<span id="LC230" 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;">i</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;">i</span><span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</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="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;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC234" 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: teal;">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>
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<pre style="margin: 0;">-<span id="LC235" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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 class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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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;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<td class="diff-line-num new new_line" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Modules</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.FastQCConfig</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.LineGraph</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceLengthDistribution</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</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="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">graphCounts</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="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">calculated</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="LC39" class="line" lang="java"> </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC42" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">LineGraph</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">},</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence Length (bp)"</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="s" style="color: #d14;">"Sequence Length"</span><span class="o" style="font-weight: 600;">},</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Distribution of sequence lengths over all sequences"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> </span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calculateDistribution</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxLen</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="LC60" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLen</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="LC61" class="line" lang="java"> <span class="n" style="color: #333;">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>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Find the min and max lengths</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" 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;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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>
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66
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<pre style="margin: 0;">+<span id="LC66" 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;">minLen</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>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">minLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">maxLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We put one extra category either side of the actual size</span></span>
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<pre style="margin: 0;">+<span id="LC74" 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;">minLen</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;">minLen</span><span class="o" style="font-weight: 600;">--;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC77" 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;">startAndInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSizeDistribution</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLen</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Work out how many categories we need</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">categories</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currentValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startAndInterval</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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82
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<pre style="margin: 0;">+<span id="LC82" 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;">currentValue</span><span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">categories</span><span class="o" style="font-weight: 600;">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="n" style="color: #333;">currentValue</span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">startAndInterval</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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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">graphCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</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;">categories</span><span class="o" style="font-weight: 600;">];</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">categories</span><span class="o" style="font-weight: 600;">];</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> </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;">minValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startAndInterval</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;">startAndInterval</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;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">startAndInterval</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;">startAndInterval</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;">i</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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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" 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;">maxValue</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxLen</span><span class="o" style="font-weight: 600;">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" 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;">bp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">minValue</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">maxValue</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" 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;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">];</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" 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;">startAndInterval</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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;">minValue</span><span class="o" style="font-weight: 600;">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minValue</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;">maxValue</span><span class="o" style="font-weight: 600;">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" 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;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequence</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" 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;">seqLen</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;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">newLengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seqLen</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>
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122
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<pre style="margin: 0;">+<span id="LC122" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">newLengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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124
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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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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLengthCounts</span><span class="o" style="font-weight: 600;">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> </span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seqLen</span><span class="o" style="font-weight: 600;">];</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">getSizeDistribution</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;">min</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;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We won't group if they've asked us not to</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" 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;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">nogroup</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">min</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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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</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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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" 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;">base</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="n" style="color: #333;">base</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>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">starting</span><span class="o" style="font-weight: 600;">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"></span>
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148
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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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</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 class="mi" style="color: #099;">2</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>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="nl">OUTER:</span> <span class="k" style="font-weight: 600;">while</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="o" style="font-weight: 600;">{</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> </span>
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152
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<pre style="margin: 0;">+<span id="LC152" 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;">d</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;">d</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tester</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divisions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">];</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" 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;">max</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">interval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span> <span class="n" style="color: #333;">OUTER</span><span class="o" style="font-weight: 600;">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;">base</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>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> </span>
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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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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we work out the first value to be plotted</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">basicDivision</span> <span class="o" style="font-weight: 600;">=</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;">min</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">testStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basicDivision</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> </span>
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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;">starting</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">testStart</span><span class="o" style="font-weight: 600;">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">starting</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">};</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> </span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> </span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> </span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="n" style="color: #333;">lengthCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</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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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Shows the distribution of sequence length over all sequences"</span><span class="o" style="font-weight: 600;">;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Sequence Length Distribution"</span><span class="o" style="font-weight: 600;">;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> </span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if they've turned this test off</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" 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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</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="o" style="font-weight: 600;">{</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" 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">
198
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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;">lengthCounts</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
205
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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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" 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 class="c1" style="color: #998; font-style: italic;">// See if they've turned this test off</span></span>
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208
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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;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequence_length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</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="o" style="font-weight: 600;">{</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java"> </span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Warn if they're not all the same length</span></span>
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<td class="diff-line-num new new_line" 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">
213
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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;">seenLength</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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<td class="diff-line-num new new_line" 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">
214
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<pre style="margin: 0;">+<span id="LC214" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
215
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<pre style="margin: 0;">+<span id="LC215" 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;">lengthCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
216
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<pre style="margin: 0;">+<span id="LC216" 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;">seenLength</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" 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">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java"> <span class="n" style="color: #333;">seenLength</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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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java"></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">calculateDistribution</span><span class="o" style="font-weight: 600;">();</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java"></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"sequence_length_distribution.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Sequence length distribution"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">800</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">),</span> <span class="mi" style="color: #099;">600</span><span class="o" style="font-weight: 600;">);</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> </span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java"> <span class="n" style="color: #333;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Length\tCount\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" 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;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Remove any padding we added to make the graph look better</span></span>
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<td class="diff-line-num new new_line" 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">
236
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<pre style="margin: 0;">+<span id="LC236" 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;">i</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;">i</span><span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="o" style="font-weight: 600;">{</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" 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">
239
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<pre style="margin: 0;">+<span id="LC239" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xCategories</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" 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: teal;">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>
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241
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<pre style="margin: 0;">+<span id="LC241" 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: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" 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: teal;">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>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java"></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/fastqc/compare/305676606707d1438970e75d47bc924493886ff6...8759cc9268ed944d4805ce2639b5fb0643bf35e4#3013cb0481f38b744114f30dd2156d353af7ebf7"><strong>uk/ac/babraham/FastQC/Results/ResultsPanel.java</strong></a>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Results</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.BorderLayout</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Color</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Component</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.DefaultListCellRenderer</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.ImageIcon</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JList</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JScrollPane</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.ListSelectionModel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ListSelectionEvent</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ListSelectionListener</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Analysis.AnalysisListener</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ResultsPanel</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">JPanel</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">ListSelectionListener</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">AnalysisListener</span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">ERROR_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/error.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">WARNING_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/warning.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">OK_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/tick.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JList</span> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JPanel</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JPanel</span> <span class="n" style="color: #333;">currentPanel</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="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JLabel</span> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">ResultsPanel</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequenceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="n" style="color: #333;">setLayout</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Waiting to start..."</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">valueChanged</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ListSelectionEvent</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSelectedIndex</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">index</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>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">);</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="n" style="color: #333;">currentPanel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">];</span> </span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="n" style="color: #333;">validate</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">repaint</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceFile</span> <span class="nf" style="color: #900; font-weight: 600;">sequenceFile</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleRenderer</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">DefaultListCellRenderer</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Component</span> <span class="nf" style="color: #900; font-weight: 600;">getListCellRendererComponent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">JList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Object</span> <span class="n" style="color: #333;">value</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;">index</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;">isSelected</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;">cellHasFocus</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getListCellRendererComponent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isSelected</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cellHasFocus</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> </span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">QCModule</span> <span class="n" style="color: #333;">module</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">;</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OK_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" 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;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">raisesError</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ERROR_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" 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;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">raisesWarning</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WARNING_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="java"> <span class="n" style="color: #333;">JLabel</span> <span class="n" style="color: #333;">returnLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">name</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">icon</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LEFT</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setOpaque</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="LC99" 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;">isSelected</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setBackground</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setBackground</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisComplete</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">modulesToDisplay</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC116" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC117" 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;">rawModules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">ignoreInReport</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="n" style="color: #333;">modulesToDisplay</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> </span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modulesToDisplay</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">QCModule</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="LC123" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">panels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JPanel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> </span>
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126
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<pre style="margin: 0;">-<span id="LC126" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">getResultsPanel</span><span class="o" style="font-weight: 600;">();</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> </span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">);</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setCellRenderer</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ModuleRenderer</span><span class="o" style="font-weight: 600;">());</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setSelectionMode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ListSelectionModel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SINGLE_SELECTION</span><span class="o" style="font-weight: 600;">);</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setSelectedIndex</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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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addListSelectionListener</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> </span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JScrollPane</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WEST</span><span class="o" style="font-weight: 600;">);</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">currentPanel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">panels</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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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="n" style="color: #333;">validate</span><span class="o" style="font-weight: 600;">();</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> </span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisUpdated</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</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;">sequencesProcessed</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;">percentComplete</span><span class="o" style="font-weight: 600;">)</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">percentComplete</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">99</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Read "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sequencesProcessed</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" sequences"</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Read "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sequencesProcessed</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" sequences ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</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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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisExceptionReceived</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process file: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLocalizedMessage</span><span class="o" style="font-weight: 600;">());</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisStarted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Starting analysis..."</span><span class="o" style="font-weight: 600;">);</span> </span>
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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>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> </span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Results</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.BorderLayout</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Color</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Component</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.DefaultListCellRenderer</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.ImageIcon</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JList</span><span class="o" style="font-weight: 600;">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JScrollPane</span><span class="o" style="font-weight: 600;">;</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.ListSelectionModel</span><span class="o" style="font-weight: 600;">;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ListSelectionEvent</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ListSelectionListener</span><span class="o" style="font-weight: 600;">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Analysis.AnalysisListener</span><span class="o" style="font-weight: 600;">;</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ResultsPanel</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">JPanel</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">ListSelectionListener</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">AnalysisListener</span><span class="o" style="font-weight: 600;">{</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">ERROR_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/error.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">WARNING_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/warning.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">OK_ICON</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ImageIcon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ClassLoader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSystemResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"uk/ac/babraham/FastQC/Resources/tick.png"</span><span class="o" style="font-weight: 600;">));</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> </span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JList</span> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JPanel</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JPanel</span> <span class="n" style="color: #333;">currentPanel</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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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">JLabel</span> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> </span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">ResultsPanel</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequenceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="n" style="color: #333;">setLayout</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">());</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Waiting to start..."</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">valueChanged</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ListSelectionEvent</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSelectedIndex</span><span class="o" style="font-weight: 600;">();</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" 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;">index</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>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="n" style="color: #333;">currentPanel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">];</span> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="n" style="color: #333;">validate</span><span class="o" style="font-weight: 600;">();</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">repaint</span><span class="o" style="font-weight: 600;">();</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceFile</span> <span class="nf" style="color: #900; font-weight: 600;">sequenceFile</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> </span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleRenderer</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">DefaultListCellRenderer</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Component</span> <span class="nf" style="color: #900; font-weight: 600;">getListCellRendererComponent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">JList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Object</span> <span class="n" style="color: #333;">value</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;">index</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;">isSelected</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;">cellHasFocus</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getListCellRendererComponent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isSelected</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cellHasFocus</span><span class="o" style="font-weight: 600;">);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">QCModule</span> <span class="n" style="color: #333;">module</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">ImageIcon</span> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OK_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" 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;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">raisesError</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ERROR_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" 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;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">raisesWarning</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="n" style="color: #333;">icon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WARNING_ICON</span><span class="o" style="font-weight: 600;">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">JLabel</span> <span class="n" style="color: #333;">returnLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">module</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">name</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">icon</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">JLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LEFT</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setOpaque</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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99
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<pre style="margin: 0;">+<span id="LC99" 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;">isSelected</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setBackground</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LIGHT_GRAY</span><span class="o" style="font-weight: 600;">);</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setBackground</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WHITE</span><span class="o" style="font-weight: 600;">);</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">returnLabel</span><span class="o" style="font-weight: 600;">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisComplete</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">modulesToDisplay</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">QCModule</span><span class="o" style="font-weight: 600;">>();</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" 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;">rawModules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">ignoreInReport</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="n" style="color: #333;">modulesToDisplay</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rawModules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">]);</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modulesToDisplay</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">QCModule</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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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">panels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JPanel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> </span>
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126
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<pre style="margin: 0;">+<span id="LC126" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Getting panel for "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">name</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">" with "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">description</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="n" style="color: #333;">panels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">getResultsPanel</span><span class="o" style="font-weight: 600;">();</span></span>
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129
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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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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setCellRenderer</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ModuleRenderer</span><span class="o" style="font-weight: 600;">());</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setSelectionMode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ListSelectionModel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SINGLE_SELECTION</span><span class="o" style="font-weight: 600;">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setSelectedIndex</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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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addListSelectionListener</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">JScrollPane</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">moduleList</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">WEST</span><span class="o" style="font-weight: 600;">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="n" style="color: #333;">currentPanel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">panels</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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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentPanel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">BorderLayout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CENTER</span><span class="o" style="font-weight: 600;">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="n" style="color: #333;">validate</span><span class="o" style="font-weight: 600;">();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> </span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisUpdated</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</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;">sequencesProcessed</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;">percentComplete</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" 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;">percentComplete</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">99</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Read "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sequencesProcessed</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" sequences"</span><span class="o" style="font-weight: 600;">);</span> </span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Read "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sequencesProcessed</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" sequences ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</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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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisExceptionReceived</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process file: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLocalizedMessage</span><span class="o" style="font-weight: 600;">());</span></span>
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156
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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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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisStarted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">progressLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setText</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Starting analysis..."</span><span class="o" style="font-weight: 600;">);</span> </span>
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160
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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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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java"> </span>
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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></pre>
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