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Dylan Aïssi pushed to branch master at <a href="https://salsa.debian.org/med-team/chromhmm">Debian Med / chromhmm</a>
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Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/d70bc9dae0d6d3b51a0ba2f5cb615d191c84875c">d70bc9da</a></strong>
<div>
<span> by Dylan Aïssi </span> <i> at 2025-02-03T21:58:33+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.26+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/660e46dd4a48da684828f94fddb43cfe5d830b8c">660e46dd</a></strong>
<div>
<span> by Dylan Aïssi </span> <i> at 2025-02-03T21:58:53+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.26+dfsg'
Update to upstream version '1.26+dfsg'
with Debian dir 786d6ba439483c15337149d07e707349e45c37ec</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/f5925e900611cf11d3e8ced252af20edb77bd063">f5925e90</a></strong>
<div>
<span> by Dylan Aïssi </span> <i> at 2025-02-03T22:05:55+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Bump debian/changelog
</pre>
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<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/075ad1c2258313742856f695ee7e29d163cbda5b">075ad1c2</a></strong>
<div>
<span> by Dylan Aïssi </span> <i> at 2025-02-03T22:08:48+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.0 (no changes required)
</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
6 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e1a765a5b2b828119bc810319c6fa07e7300eecf">
edu/mit/compbio/ChromHMM/ChromHMM.java
</a>
</li>
<li class="file-stats">
<a href="#4fb31ca7c49b2c49cfd549091ba94777db11f494">
edu/mit/compbio/ChromHMM/StateAnalysis.java
</a>
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<li class="file-stats">
<a href="#6f75f608cf26f055e686012013a437ab1cfcdfed">
versionlog.txt
</a>
</li>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong style="font-weight: 600;">README.md</strong></a>
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See https://ernstlab.<span class="idiff left right deletion" style="background-color: #fac5cd;">biolchem.ucla.edu</span>/ChromHMM/ for more information on ChromHMM.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See https://ernstlab.<span class="idiff left right addition" style="background-color: #c7f0d2;">github.io</span>/ChromHMM/ for more information on ChromHMM.</span></span>
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2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span></pre></td>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: 600;">debian/changelog</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">chromhmm (1.26+dfsg-1) UNRELEASED; urgency=medium</span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"> * Exclude build on i386</span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"> [ Dylan Aïssi ]</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext"> * New upstream version 1.26+dfsg</span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.7.0 (no changes required)</span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Mon, 03 Feb 2025 22:05:13 +0100</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext">chromhmm (1.25+dfsg-1) unstable; urgency=medium</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong style="font-weight: 600;">debian/control</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext"> libbatik-java,</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="plaintext"> libjheatchart-java</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="plaintext">Build-Depends-Indep: default-jdk</span>
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right deletion" style="background-color: #fac5cd;">6.2</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right addition" style="background-color: #c7f0d2;">7.0</span></span>
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/chromhmm</span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/chromhmm.git</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="plaintext">Homepage: https://compbio.mit.edu/ChromHMM/</span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#e1a765a5b2b828119bc810319c6fa07e7300eecf"><strong style="font-weight: 600;">edu/mit/compbio/ChromHMM/ChromHMM.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5977" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -5977,6 +5977,13 @@ public class ChromHMM</td>
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5977
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5977" 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: #333333;">objMaxCoord</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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5978
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5978
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5978" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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5979
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<td class="new_line diff-line-num" data-linenumber="5979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5979
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5979" class="line" lang="java"> <span class="n" style="color: #333333;">nlastcoordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">numtime_nseq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,((</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">objMaxCoord</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5980" class="line" lang="java"></span>
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5981
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5981" 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: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5982" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5982
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5982" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5983" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5983
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5983" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5984" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5984
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5984" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Start of interval "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">" (1-based) is past the end of the chromosome "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5985
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5985" class="line" lang="java"> <span class="s" style="color: #dd1144;">"; Check if chromosome length file given to LearnModel is the same used for the binarization"</span><span class="o" style="font-weight: 600;">);</span></span>
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5986
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5986" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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5980
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5987
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5987" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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5981
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5988
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5988" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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5982
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<td class="new_line diff-line-num" data-linenumber="5989" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5989
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5989" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -6114,6 +6121,13 @@ public class ChromHMM</td>
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6114
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<td class="new_line diff-line-num" data-linenumber="6121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6121" 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: #333333;">objMaxCoord</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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6115
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6122
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6122" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="6116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6116
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<td class="new_line diff-line-num" data-linenumber="6123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6123
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6123" class="line" lang="java"> <span class="n" style="color: #333333;">nlastcoordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">numtime_nseq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,((</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">objMaxCoord</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">());</span></span>
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6124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6124" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="6125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6125" 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: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">)</span></span>
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6126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6126" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6127" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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6128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6128" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Start of interval "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">" (1-based) is past the end of the chromosome "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">+</span></span>
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6129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6129" class="line" lang="java"> <span class="s" style="color: #dd1144;">"; Check if chromosome length file given to LearnModel is the same used for the binarization"</span><span class="o" style="font-weight: 600;">);</span></span>
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6130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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6117
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6131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6131" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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6118
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6132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6132" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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6119
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6133
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6133" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7061" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7075" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -7061,13 +7075,20 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="7061" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7061
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<td class="new_line diff-line-num" data-linenumber="7075" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7075
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7075" 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: #333333;">objMaxCoord</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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7062
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<td class="new_line diff-line-num" data-linenumber="7076" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7076
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7076" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7063" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7063
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<td class="new_line diff-line-num" data-linenumber="7077" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7077
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7077" class="line" lang="java"> <span class="n" style="color: #333333;">nlastcoordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">numtime_nseq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,((</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">objMaxCoord</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">());</span></span>
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7078
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7078" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="7079" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7079
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7079" 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: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">)</span></span>
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7080
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7080" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7081" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7081
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7081" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7082" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7082
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7082" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Start of interval "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">" (1-based) is past the end of the chromosome "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7083" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7083
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7083" class="line" lang="java"> <span class="s" style="color: #dd1144;">"; Check if chromosome length file given to LearnModel is the same used for the binarization"</span><span class="o" style="font-weight: 600;">);</span></span>
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7084
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7084" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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7064
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7085
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7085" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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7065
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<td class="new_line diff-line-num" data-linenumber="7086" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7086
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7086" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="7066" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7066
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<td class="new_line diff-line-num" data-linenumber="7087" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7087
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7087" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7067" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7067
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<td class="new_line diff-line-num" data-linenumber="7088" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7088
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7088" class="line" lang="java"> <span class="n" style="color: #333333;">nlastcoordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">numtime_nseq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>
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7068
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<td class="new_line diff-line-num" data-linenumber="7089" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7089
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7089" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="7069" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7069
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<td class="new_line diff-line-num" data-linenumber="7090" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7090
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7090" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//pwbed.println(chromSeq[nordered_nseq]+"\t"+(nstart*nbinsize)+"\t"+nlastcoordinate+"\t"+chorder+(nmaxstateprev+1));</span></span>
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7070
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<td class="new_line diff-line-num old" data-linenumber="7091" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7070" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="7071" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7091" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7091
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7091" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="7071" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7071
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<td class="new_line diff-line-num" data-linenumber="7092" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7092
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7092" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szactualchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nmaxstateprev</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="7072" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7072
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<td class="new_line diff-line-num" data-linenumber="7093" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7093
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7093" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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7073
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<td class="new_line diff-line-num" data-linenumber="7094" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7094
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7094" class="line" lang="java"> <span class="n" style="color: #333333;">pwbedzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">btformat</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">btformat</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -7197,6 +7218,13 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="7197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7197
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<td class="new_line diff-line-num" data-linenumber="7218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7218
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7218" 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: #333333;">objMaxCoord</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="7198" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7198
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<td class="new_line diff-line-num" data-linenumber="7219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7219
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7219" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7199
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<td class="new_line diff-line-num" data-linenumber="7220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7220
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7220" class="line" lang="java"> <span class="n" style="color: #333333;">nlastcoordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">numtime_nseq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,((</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">objMaxCoord</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7221" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="7200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7222" 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: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7223" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7224" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7224" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7225" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Start of interval "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #dd1144;">" (1-based) is past the end of the chromosome "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nlastcoordinate</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7226" class="line" lang="java"> <span class="s" style="color: #dd1144;">"; Check if chromosome length file given to LearnModel is the same used for the binarization"</span><span class="o" style="font-weight: 600;">);</span></span>
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7227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7227" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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7200
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7228
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7228" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="7201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7201
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<td class="new_line diff-line-num" data-linenumber="7229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7229
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7229" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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7202
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<td class="new_line diff-line-num" data-linenumber="7230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7230
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7230" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -13359,7 +13387,7 @@ public class ChromHMM</td>
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13359
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<td class="new_line diff-line-num" data-linenumber="13387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13387
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13387" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="13360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13360
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<td class="new_line diff-line-num" data-linenumber="13388" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13388
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13388" 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: #333333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Version"</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="13361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13361
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<td class="new_line diff-line-num" data-linenumber="13389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13389" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13362
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<td class="new_line diff-line-num old" data-linenumber="13390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13362" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"This is Version 1.2<span class="idiff left right deletion" style="background-color: #fac5cd;">5</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="13363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13390" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"This is Version 1.2<span class="idiff left right addition" style="background-color: #c7f0d2;">6</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>
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13363
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<td class="new_line diff-line-num" data-linenumber="13391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13391
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13391" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="13364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13364
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<td class="new_line diff-line-num" data-linenumber="13392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13392
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13392" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">))||(</span><span class="n" style="color: #333333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"BinarizeBed"</span><span class="o" style="font-weight: 600;">)))</span></span>
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13365
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13393
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13393" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14565" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14537,6 +14565,8 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="14537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14537
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<td class="new_line diff-line-num" data-linenumber="14565" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14565
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14565" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blowmem</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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14538
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<td class="new_line diff-line-num" data-linenumber="14566" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14566
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14566" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="14539" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14539
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<td class="new_line diff-line-num" data-linenumber="14567" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14567
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14567" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="14540" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14568" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14568
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14568" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blogpvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14569" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14569
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14569" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="14540" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14540
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<td class="new_line diff-line-num" data-linenumber="14570" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14570
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14570" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nr</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULTCOLOR_R</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="14541" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14541
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<td class="new_line diff-line-num" data-linenumber="14571" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14571
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14571" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">ng</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULTCOLOR_G</span><span class="o" style="font-weight: 600;">;</span></span>
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14542
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<td class="new_line diff-line-num" data-linenumber="14572" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14572
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14572" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nb</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULTCOLOR_B</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14586" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14616" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14586,6 +14616,10 @@ public class ChromHMM</td>
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14586
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<td class="new_line diff-line-num" data-linenumber="14616" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14616
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14616" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="14587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14587
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<td class="new_line diff-line-num" data-linenumber="14617" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14617
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14617" class="line" lang="java"> <span class="n" style="color: #333333;">szinputcoordlist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">args</span><span class="o" style="font-weight: 600;">[++</span><span class="n" style="color: #333333;">nargindex</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="14588" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14588
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<td class="new_line diff-line-num" data-linenumber="14618" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14618
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14618" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="14589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14619" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14619
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14619" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"-nopvals"</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="14589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14620" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14620
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14620" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="14589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14621" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14621
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14621" class="line" lang="java"> <span class="n" style="color: #333333;">blogpvals</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="old_line diff-line-num new" data-linenumber="14589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14622" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14622
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14622" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="14589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14589
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<td class="new_line diff-line-num" data-linenumber="14623" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14623
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14623" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"-signal"</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="14590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14590
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<td class="new_line diff-line-num" data-linenumber="14624" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14624
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14624" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="14591" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14591
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<td class="new_line diff-line-num" data-linenumber="14625" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14625
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14625" class="line" lang="java"> <span class="n" style="color: #333333;">busesignal</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14661,18 +14695,18 @@ public class ChromHMM</td>
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14661
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14695
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14695" 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: #333333;">blowmem</span><span class="o" style="font-weight: 600;">)</span></span>
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14662
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14696
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14696" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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14663
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<td class="new_line diff-line-num" data-linenumber="14697" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14697
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14697" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">StateAnalysis</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">enrichmentMaxLowMem</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szinput</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szinputcoordlist</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="14664" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14664
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<td class="new_line diff-line-num old" data-linenumber="14698" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14664" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14698" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14698
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14698" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;">);</span></span>
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14665
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14699
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14699" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14666
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<td class="new_line diff-line-num" data-linenumber="14700" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14700
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14700" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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14667
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14701
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14701" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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14668
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<td class="new_line diff-line-num" data-linenumber="14702" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14702
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14702" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">StateAnalysis</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">enrichmentMax</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szinput</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szinputcoordlist</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span> </span>
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14669
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<td class="new_line diff-line-num old" data-linenumber="14703" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14669" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">);</span></span>
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14703
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14703" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;">);</span></span>
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14704
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14704" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14671
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14705
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14705" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14672
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<td class="new_line diff-line-num" data-linenumber="14706" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14706
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14706" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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14673
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<td class="new_line diff-line-num" data-linenumber="14707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14707
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14707" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="14674" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14674
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<td class="new_line diff-line-num" data-linenumber="14708" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14708
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14708" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">StateAnalysis</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">enrichmentPosterior</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szinput</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szinputcoordlist</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14675" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14675
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<td class="new_line diff-line-num old" data-linenumber="14709" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14675" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="14676" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14709" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14709
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14709" class="line" lang="java"> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;">);</span></span>
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14676
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<td class="new_line diff-line-num" data-linenumber="14710" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14710
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14710" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14677
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14711
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14711" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14678
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<td class="new_line diff-line-num" data-linenumber="14712" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14712
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14712" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14684" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14718" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14684,8 +14718,8 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="14684" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14684
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<td class="new_line diff-line-num" data-linenumber="14718" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14718
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14718" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="14685" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14685
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<td class="new_line diff-line-num" data-linenumber="14719" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14719
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14719" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"usage OverlapEnrichment [-a cell][-b binsize][-binres][-browser][-color r,g,b][-center][-colfields chromosome,start,end[,signal]]"</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="old_line diff-line-num" data-linenumber="14686" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14686
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<td class="new_line diff-line-num" data-linenumber="14720" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14720
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14720" class="line" lang="java"> <span class="s" style="color: #dd1144;">"[-e offsetend][-f coordlistfile][-labels][-lowmem][-m labelmappingfile]"</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14687" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14687
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<td class="new_line diff-line-num old" data-linenumber="14721" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14687" class="line" lang="java"> <span class="s" style="color: #dd1144;">"[-multicount][-noimage][-posterior][-s offsetstart][-signal][-t title][-uniformscale]"</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14688" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14688
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<td class="new_line diff-line-num old" data-linenumber="14721" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14688" class="line" lang="java"> <span class="s" style="color: #dd1144;">" inputsegment inputcoorddir outfileprefix"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="14689" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14721" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14721
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14721" class="line" lang="java"> <span class="s" style="color: #dd1144;">"[-multicount][-noimage][-<span class="idiff left right addition" style="background-color: #c7f0d2;">nopvals][-</span>posterior][-s offsetstart][-signal][-t title][-uniformscale]"</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14722" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14722
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14722" class="line" lang="java"> <span class="s" style="color: #dd1144;">" inputsegment inputcoorddir outfileprefix"</span><span class="o" style="font-weight: 600;">);</span><span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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14689
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14723
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14723" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14690
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<td class="new_line diff-line-num" data-linenumber="14724" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14724
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14724" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="14691" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14691
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<td class="new_line diff-line-num" data-linenumber="14725" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14725
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14725" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"NeighborhoodEnrichment"</span><span class="o" style="font-weight: 600;">))||(</span><span class="n" style="color: #333333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"NeighborhoodSignal"</span><span class="o" style="font-weight: 600;">)))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -15391,7 +15425,7 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="15391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15391
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<td class="new_line diff-line-num" data-linenumber="15425" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15425
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15425" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BCENTER</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BCOUNTMULTI</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num" data-linenumber="15392" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15392
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<td class="new_line diff-line-num" data-linenumber="15426" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15426
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15426" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUSESIGNAL</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="c1" style="color: #999988; font-style: italic;">//szcolfields,</span></span>
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<td class="old_line diff-line-num" data-linenumber="15393" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15393
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<td class="new_line diff-line-num" data-linenumber="15427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15427
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15427" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BBASERES</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutputdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZOVERLAPEXTENSION</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15394
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<td class="new_line diff-line-num old" data-linenumber="15428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15394" class="line" lang="java"> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"Fold Enrichment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</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: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="15395" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="15428" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15428" class="line" lang="java"> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"Fold Enrichment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</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: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">false</span></span><span class="o" style="font-weight: 600;">);</span></span>
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15395
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<td class="new_line diff-line-num" data-linenumber="15429" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15429
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15429" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="15396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15396
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<td class="new_line diff-line-num" data-linenumber="15430" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15430
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15430" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="15397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15397
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<td class="new_line diff-line-num" data-linenumber="15431" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15431
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15431" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15437" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -15403,7 +15437,7 @@ public class ChromHMM</td>
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<td class="old_line diff-line-num" data-linenumber="15403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15403
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<td class="new_line diff-line-num" data-linenumber="15437" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15437" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BCENTER</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BCOUNTMULTI</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num" data-linenumber="15404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15404
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<td class="new_line diff-line-num" data-linenumber="15438" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15438
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15438" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUSESIGNAL</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="c1" style="color: #999988; font-style: italic;">//szcolfields,</span></span>
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<td class="old_line diff-line-num" data-linenumber="15405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15405
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<td class="new_line diff-line-num" data-linenumber="15439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15439
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15439" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BBASERES</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">szoutputdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZOVERLAPEXTENSION</span><span class="o" style="font-weight: 600;">,</span></span>
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15406
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15406" class="line" lang="java"> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"Fold Enrichment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</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: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15440" class="line" lang="java"> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"Fold Enrichment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szprefix</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: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">false</span></span><span class="o" style="font-weight: 600;">);</span></span>
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15407
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15441
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15441" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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15408
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<td class="new_line diff-line-num" data-linenumber="15442" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15442
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15442" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoverlapoutfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZOVERLAPEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">".txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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15409
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15443
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15443" 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: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span></span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#4fb31ca7c49b2c49cfd549091ba94777db11f494"><strong style="font-weight: 600;">edu/mit/compbio/ChromHMM/StateAnalysis.java</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -38,6 +38,11 @@ public class StateAnalysis</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="no" style="color: #008080;">EPSILONOVERLAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">0.00000001</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="java"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Limit on how significant p-value should be reported in OverlapEnrichment</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="no" style="color: #008080;">PVALLOG10CUTOFF</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">300</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * A record for storing a segmentation</span></span>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -200,7 +205,8 @@ public class StateAnalysis</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC205" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">enrichmentPosterior</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szposteriordir</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcell</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szinputcoordlist</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
201
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206
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC206" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
207
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC207" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> </span>
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203
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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC203" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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204
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<td class="new_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
210
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC210" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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212
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC212" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="542" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -542,7 +548,8 @@ public class StateAnalysis</td>
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542
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548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC548" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
543
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<td class="new_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
549
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC549" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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544
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550
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC550" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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545
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<td class="new_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC545" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
551
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC551" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//update in v1.26</span></span>
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552
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC552" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">1.0</span><span class="o" style="font-weight: 600;">/(</span><span class="kt" style="color: #445588; 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: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC555" 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: #333333;">bcenter</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="647" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -640,7 +647,7 @@ public class StateAnalysis</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC647" class="line" lang="java"></span>
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648
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC648" class="line" lang="java"></span>
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<td class="new_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
649
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC649" class="line" lang="java"> <span class="n" style="color: #333333;">outputenrichment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">),</span></span>
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643
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC643" class="line" lang="java"> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
650
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC650" class="line" lang="java"> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bcenter</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&&</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,!</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bunique</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nbinsize</span></span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC652" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="667" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="674" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -667,7 +674,8 @@ public class StateAnalysis</td>
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674
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC674" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span></span>
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675
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC675" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span></span>
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676
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC676" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="670" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
670
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<td class="new_line diff-line-num old" data-linenumber="677" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC670" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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<td class="old_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
677
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC677" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
678
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC678" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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<td class="old_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
671
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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
679
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC679" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="672" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
672
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<td class="new_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
680
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC680" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//usual high memory</span></span>
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<td class="old_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
673
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<td class="new_line diff-line-num" data-linenumber="681" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
681
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC681" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333333;">alsegments</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;">();</span> <span class="c1" style="color: #999988; font-style: italic;">//stores all the segments</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1131,7 +1139,8 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1131
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<td class="new_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1132
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<td class="new_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1140" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="1133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1133
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<td class="new_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1141" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1134
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<td class="new_line diff-line-num old" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1134" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1142" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//fix in v1.26</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1143" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">1.0</span><span class="o" style="font-weight: 600;">/(</span><span class="kt" style="color: #445588; 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: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">);</span></span>
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1135
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<td class="new_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1136
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<td class="new_line diff-line-num" data-linenumber="1145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1145
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1145" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1137
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<td class="new_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1146" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Integer</span> <span class="n" style="color: #333333;">objChrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">hmchromToIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1216,7 +1225,7 @@ public class StateAnalysis</td>
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1216
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<td class="new_line diff-line-num" data-linenumber="1225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1225" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1217
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<td class="new_line diff-line-num" data-linenumber="1226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1226
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1226" class="line" lang="java"> <span class="n" style="color: #333333;">outputenrichment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1218
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<td class="new_line diff-line-num" data-linenumber="1227" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1227
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1227" class="line" lang="java"> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)),</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="1219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1219
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<td class="new_line diff-line-num old" data-linenumber="1228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1219" class="line" lang="java"> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1228" class="line" lang="java"> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bcenter</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&&</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">!</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bunique</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nbinsize</span></span><span class="o" style="font-weight: 600;">);</span></span>
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1220
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<td class="new_line diff-line-num" data-linenumber="1229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1229
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1229" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1221
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1230
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1230" class="line" lang="java"></span>
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1222
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<td class="new_line diff-line-num" data-linenumber="1231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1231
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1231" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1245,8 +1254,9 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1245
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<td class="new_line diff-line-num" data-linenumber="1254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1254
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1254" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">enrichmentMaxLowMem</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szinputsegment</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szinputcoorddir</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szinputcoordlist</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1246
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<td class="new_line diff-line-num" data-linenumber="1255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1255
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1255" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetleft</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetright</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1247
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<td class="new_line diff-line-num" data-linenumber="1256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1256" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcenter</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bunique</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1248
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<td class="new_line diff-line-num old" data-linenumber="1257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1248" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="1249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1249
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<td class="new_line diff-line-num old" data-linenumber="1257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1249" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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1257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1257" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbaseres</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1258" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1259" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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1250
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<td class="new_line diff-line-num" data-linenumber="1260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1260
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1260" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1251
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1261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1261" class="line" lang="java"></span>
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1252
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1262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1262" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1803" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1813" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1803,7 +1813,8 @@ public class StateAnalysis</td>
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1803
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<td class="new_line diff-line-num" data-linenumber="1813" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1813
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1813" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1804" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1804
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<td class="new_line diff-line-num" data-linenumber="1814" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1814
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1814" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="1805" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1805
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<td class="new_line diff-line-num" data-linenumber="1815" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1815
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1815" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1806" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1806
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<td class="new_line diff-line-num old" data-linenumber="1816" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1806" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1807" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1816" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1816
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1816" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//fix in v1.26</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1807" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1817" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1817
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1817" class="line" lang="java"> <span class="n" style="color: #333333;">damount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">1.0</span><span class="o" style="font-weight: 600;">/(</span><span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>
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1807
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<td class="new_line diff-line-num" data-linenumber="1818" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1818" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1808
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<td class="new_line diff-line-num" data-linenumber="1819" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1819
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1819" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1809" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1809
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<td class="new_line diff-line-num" data-linenumber="1820" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1820
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1820" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//Integer objChrom = (Integer) hmchromToIndex.get(szchrom);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1901" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1890,7 +1901,7 @@ public class StateAnalysis</td>
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1890
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<td class="new_line diff-line-num" data-linenumber="1901" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1901
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1901" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1891
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1902
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1902" class="line" lang="java"></span>
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1892
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1903
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1903" class="line" lang="java"> <span class="n" style="color: #333333;">outputenrichment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1893
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<td class="new_line diff-line-num old" data-linenumber="1904" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1893" class="line" lang="java"> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)),</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1904" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1904
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1904" class="line" lang="java"> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)),</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szlabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bcenter</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&&</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">blogpvals</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">!</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">bunique</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nbinsize</span></span><span class="o" style="font-weight: 600;">);</span></span>
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1894
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1905
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1905" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1895
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1906
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1906" class="line" lang="java"></span>
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1896
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1907
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1907" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1932" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1943" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1932,7 +1943,8 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1932" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1932
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<td class="new_line diff-line-num" data-linenumber="1943" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1943
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1943" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1933" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1933
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<td class="new_line diff-line-num" data-linenumber="1944" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1944
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1944" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1934" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1934
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<td class="new_line diff-line-num" data-linenumber="1945" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1945
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1945" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">char</span> <span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1935" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1935
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<td class="new_line diff-line-num old" data-linenumber="1946" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1935" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">HashMap</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1936" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1946" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1946
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1946" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #445588; font-weight: 600;">HashMap</span> <span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1936" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1947" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1947
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1947" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbinomial</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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<td class="old_line diff-line-num" data-linenumber="1936" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1936
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<td class="new_line diff-line-num" data-linenumber="1948" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1948
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1948" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1937
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<td class="new_line diff-line-num" data-linenumber="1949" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1949
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1949" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1938" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1938
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<td class="new_line diff-line-num" data-linenumber="1950" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1950
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1950" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">HashMap</span> <span class="n" style="color: #333333;">hmlabelExtend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">makeLabelMapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1956" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1968" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1956,13 +1968,50 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1956" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1956
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<td class="new_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1968
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1968" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">".txt"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1957" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1957
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<td class="new_line diff-line-num" data-linenumber="1969" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1969
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1969" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333333;">pw</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">".txt"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="1958" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1958
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<td class="new_line diff-line-num" data-linenumber="1970" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1970
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1970" class="line" lang="java"></span>
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<td class="old_line diff-line-num old" data-linenumber="1959" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1959
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<td class="new_line diff-line-num old" data-linenumber="1971" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1959" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)\tGenome %"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1971" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1971
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1971" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1972" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1972
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1972" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//added v1.26</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1973" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1973
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1973" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333333;">pwlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1974" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1974
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1974" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1975" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1975
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1975" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1976" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1976
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1976" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"_log10pvals.txt"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1977" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1977
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1977" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"_log10pvals.txt"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1978" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1978
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1978" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1979
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1979" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="1980" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1980
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1980" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//added v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1981" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1981
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1981" 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: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1982" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1982
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1982" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1983" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1983
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1983" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)\tGenome %"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1984" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1984
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1984" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1985
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1985" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1986" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1986
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1986" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1987" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1987
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1987" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)\tGenome %"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1988
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1988" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1989" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1989
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1989" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1990" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1990
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1990" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1991" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1991
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1991" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1992
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1992" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1993" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1993
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1993" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1994" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1994
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1994" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1995" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1995
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1995" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1996" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1996
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1996" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1997
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1997" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1998" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1998
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1998" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1999" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1999
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1999" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="1960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1960
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<td class="new_line diff-line-num" data-linenumber="2000" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2000
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2000" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1961" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1961
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<td class="new_line diff-line-num" data-linenumber="2001" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2001
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2001" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1962" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1962
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<td class="new_line diff-line-num" data-linenumber="2002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2002
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2002" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1963
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<td class="new_line diff-line-num" data-linenumber="2003" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2003
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2003" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1964
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<td class="new_line diff-line-num" data-linenumber="2004" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2004
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2004" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1965" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1965
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<td class="new_line diff-line-num" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2005
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2005" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2006" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2006
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2006" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2007" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2007
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2007" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2008" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2008
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2008" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2009" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2009
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2009" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2010" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2010
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2010" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2011" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2011
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2011" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2012" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2012
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2012" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2013" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2013
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2013" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2014" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2014
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2014" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1966
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<td class="new_line diff-line-num" data-linenumber="2015" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2015
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2015" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1967
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<td class="new_line diff-line-num" data-linenumber="2016" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2016
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2016" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">;</span></span>
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1968
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2017
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1976" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1976,6 +2025,19 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1976" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1976
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<td class="new_line diff-line-num" data-linenumber="2025" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2025
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2025" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapfold</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1977" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1977
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<td class="new_line diff-line-num" data-linenumber="2026" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2026
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2026" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1978" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1978
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<td class="new_line diff-line-num" data-linenumber="2027" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2027
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2027" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2028" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2028
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2028" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333333;">heatmaplogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2029" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2029
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2029" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2030" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2030
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2030" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2031" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2031
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2031" 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: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2032" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2032
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2032" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2033" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2033
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2033" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2034" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2034
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2034" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2035" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2035
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2035" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2036
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2036" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2037" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2037
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2037" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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2038
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2038" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2039
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2039" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2040
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2040" class="line" lang="java"></span>
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1979
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2041
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2041" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">numelim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1980" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1980
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<td class="new_line diff-line-num" data-linenumber="2042" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2042
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2042" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1981" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1981
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<td class="new_line diff-line-num" data-linenumber="2043" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2043
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2043" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2047" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1985,15 +2047,29 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="1985" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1985
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<td class="new_line diff-line-num" data-linenumber="2047" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2047
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2047" 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: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1986" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1986
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<td class="new_line diff-line-num" data-linenumber="2048" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2048
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2048" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1987" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1987
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<td class="new_line diff-line-num" data-linenumber="2049" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2049
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2049" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2050" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2050
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2050" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2051" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2051
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2051" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2052" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2052
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2052" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2053" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2053
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2053" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">hmIndexToLabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2054" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2054
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2054" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1988" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1988
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<td class="new_line diff-line-num" data-linenumber="2055" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2055
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2055" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1989" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1989
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<td class="new_line diff-line-num" data-linenumber="2056" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2056
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2056" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="1990" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1990
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<td class="new_line diff-line-num" data-linenumber="2057" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2057
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2057" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1991" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1991
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<td class="new_line diff-line-num" data-linenumber="2058" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2058
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2058" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2059" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2059
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2059" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2060
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2060" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2061
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2061" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2062" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2062
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2062" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1992" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1992
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<td class="new_line diff-line-num" data-linenumber="2063" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2063
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2063" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szsuffix</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1993" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1993
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<td class="new_line diff-line-num" data-linenumber="2064" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2064
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2064" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="1994" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1994
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<td class="new_line diff-line-num" data-linenumber="2065" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2065
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2065" 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: #333333;">szsuffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">hmlabelExtend</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">chorder</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">noffset</span><span class="o" style="font-weight: 600;">)))!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1995" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1995
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<td class="new_line diff-line-num" data-linenumber="2066" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2066
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2066" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1996" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1996
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<td class="new_line diff-line-num" data-linenumber="2067" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2067
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2067" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szsuffix</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2068" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2068
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2068" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2069" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2069
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2069" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2070" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2070
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2070" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2071" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2071
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2071" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szsuffix</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2072" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2072
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2072" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1997
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<td class="new_line diff-line-num" data-linenumber="2073" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2073
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2073" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1998" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1998
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<td class="new_line diff-line-num" data-linenumber="2074" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2074
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2074" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1999" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1999
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<td class="new_line diff-line-num" data-linenumber="2075" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2075
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2075" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2078" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2002,6 +2078,12 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="2002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2002
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<td class="new_line diff-line-num" data-linenumber="2078" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2078
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2078" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//only include genome % if scaling by column</span></span>
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<td class="old_line diff-line-num" data-linenumber="2003" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2003
</td>
<td class="new_line diff-line-num" data-linenumber="2079" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2079
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2079" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #999988; font-style: italic;">//first column is heatmap</span></span>
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<td class="old_line diff-line-num" data-linenumber="2004" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2004
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<td class="new_line diff-line-num" data-linenumber="2080" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2080
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2080" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]));</span></span>
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2081
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2081" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2082" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2082
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2082" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2083" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2083
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2083" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2084" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2084
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2084" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2085" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2085
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2085" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">]));</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2086
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2086" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2005
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<td class="new_line diff-line-num" data-linenumber="2087" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2087
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2087" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2006" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2006
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<td class="new_line diff-line-num" data-linenumber="2088" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2088
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2088" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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2007
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<td class="new_line diff-line-num" data-linenumber="2089" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2089
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2089" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2016" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2098" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2016,27 +2098,114 @@ public class StateAnalysis</td>
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2016
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<td class="new_line diff-line-num" data-linenumber="2098" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2098
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2098" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2017" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2017
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<td class="new_line diff-line-num" data-linenumber="2099" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2099
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2099" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dfold</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2018" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2018
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<td class="new_line diff-line-num" data-linenumber="2100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2100
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2019" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2101" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="2019" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2019
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<td class="new_line diff-line-num" data-linenumber="2102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2102" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dfold</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2103" class="line" lang="java"></span>
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2104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2104" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2105" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2106" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dlogpval</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2107" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2107" 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: #333333;">bbinomial</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2108" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2109" class="line" lang="java"> <span class="n" style="color: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">binomialtail</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">),</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2110" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2110" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2111" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2111" class="line" lang="java"> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">))/</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">10</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2112" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2113" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2114" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2115" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2116" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2117" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2117" class="line" lang="java"> <span class="n" style="color: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">hypergeometrictail</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2118" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2119" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">tallylabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">])*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2120" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333333;">nbinsize</span><span class="o" style="font-weight: 600;">)))/</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">10</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2122" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2123" 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: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">></span> <span class="no" style="color: #008080;">PVALLOG10CUTOFF</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2124" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2020" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2125" class="line" lang="java"> <span class="n" style="color: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">PVALLOG10CUTOFF</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2127" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2128" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2129" class="line" lang="java"> <span class="n" style="color: #333333;">dlogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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2130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2131" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2132" 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: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2133" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2134" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dlogpval</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2136" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2137" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2138" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dlogpval</span><span class="o" style="font-weight: 600;">;</span></span>
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2139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2140" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2141" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf5</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dlogpval</span><span class="o" style="font-weight: 600;">));</span></span>
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2142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2142" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2143" class="line" lang="java"></span>
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2020
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<td class="new_line diff-line-num" data-linenumber="2144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2021
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<td class="new_line diff-line-num" data-linenumber="2145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2145
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2145" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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2146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2146" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2147" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2148" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2149" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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2150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2150" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2022
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<td class="new_line diff-line-num" data-linenumber="2151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2151
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2023" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2023
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<td class="new_line diff-line-num" data-linenumber="2152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2152" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="2024" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2024
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<td class="new_line diff-line-num" data-linenumber="2153" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2153
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2153" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2025" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2025
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<td class="new_line diff-line-num" data-linenumber="2154" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2154
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2154" class="line" lang="java"> <span class="n" style="color: #333333;">numelim</span><span class="o" style="font-weight: 600;">++;</span></span>
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2026
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2155
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2155" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2027
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2156
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2028
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<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2028" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Base\t100"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2029" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2029
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<td class="new_line diff-line-num old" data-linenumber="2157" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2029" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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2157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2157" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2158" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2158" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//added v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2159" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2159" 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: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">)</span></span>
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2030
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<td class="new_line diff-line-num" data-linenumber="2160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2160
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2160" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2031" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2031
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<td class="new_line diff-line-num old" data-linenumber="2161" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2031" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"<span class="idiff left deletion" style="background-color: #fac5cd;">\t"</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">+</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">nf10</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">format</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="mi" style="color: #009999;"><span class="idiff deletion" style="background-color: #fac5cd;">100</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">*(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">dsumoverlaplabel</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">nfile</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">]/</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">dsumlabel</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">))</span>);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2161" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2161" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Base\t100"</span></span><span class="o" style="font-weight: 600;">);</span></span>
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2032
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<td class="new_line diff-line-num" data-linenumber="2162" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2162
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2162" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2163" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2164" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2165" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Base"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2166" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2167" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2168" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2168" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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2169
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2169" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2170
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2170" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf10</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">)));</span></span>
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2171
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2171" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2172" class="line" lang="java"></span>
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2033
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<td class="new_line diff-line-num" data-linenumber="2173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2173
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2173" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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2034
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<td class="new_line diff-line-num" data-linenumber="2174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2174
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2174" class="line" lang="java"> <span class="n" style="color: #333333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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2035
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2175
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2175" class="line" lang="java"></span>
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2176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2176" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2177" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2177" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2178
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2178" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2179" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2180" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//added v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2181" 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: #333333;">bcolscaleheat</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2182" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2183" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Base\t100"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2184" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2185" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2186" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2187" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2187" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Base"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2188" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2189" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2190" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2190" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2191
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2191" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2192" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2192
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2192" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nf10</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">100</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333333;">dsumoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333333;">dsumlabel</span><span class="o" style="font-weight: 600;">)));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2194" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2195" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2196" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2196" class="line" lang="java"> <span class="n" style="color: #333333;">pwlogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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2197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2197" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2198" class="line" lang="java"></span>
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2036
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<td class="new_line diff-line-num" data-linenumber="2199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2199
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2199" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">rowlabels</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #999988; font-style: italic;">// = new String[tallyoverlaplabel[0].length];</span></span>
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2037
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<td class="new_line diff-line-num" data-linenumber="2200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2200
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2200" 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: #333333;">numelim</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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2038
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<td class="new_line diff-line-num" data-linenumber="2201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2201
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2201" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2039" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2039
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<td class="new_line diff-line-num" data-linenumber="2202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2202" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333333;">heatmapreduce</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">numelim</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2203" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2040" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2204" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333333;">heatmapreducelogpval</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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2205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2205" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2206" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2040" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2207" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapreducelogpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">numelim</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2208" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2040
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<td class="new_line diff-line-num" data-linenumber="2209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2209
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2209" class="line" lang="java"> <span class="n" style="color: #333333;">rowlabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">heatmapreduce</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="2041" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2041
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<td class="new_line diff-line-num" data-linenumber="2210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2210
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2210" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nkeepindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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2042
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<td class="new_line diff-line-num" data-linenumber="2211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2211
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2211" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">tallyoverlaplabel</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2046" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2046,6 +2215,11 @@ public class StateAnalysis</td>
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<td class="old_line diff-line-num" data-linenumber="2046" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2046
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<td class="new_line diff-line-num" data-linenumber="2215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2215
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2215" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>
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2047
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<td class="new_line diff-line-num" data-linenumber="2216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2216
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2216" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2048" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2048
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<td class="new_line diff-line-num" data-linenumber="2217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2217
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2217" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapreduce</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nkeepindex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">ncol</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2218" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2049" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2219" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2220" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2049" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2221" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapreducelogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nkeepindex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">ncol</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">ncol</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2222" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2049
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<td class="new_line diff-line-num" data-linenumber="2223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2223
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2223" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2050
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2224" class="line" lang="java"></span>
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2225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2225" 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: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2118,6 +2292,33 @@ public class StateAnalysis</td>
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2118
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<td class="new_line diff-line-num" data-linenumber="2292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2292
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2292" class="line" lang="java"> <span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]-</span><span class="n" style="color: #333333;">dminval</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333333;">dmaxval</span><span class="o" style="font-weight: 600;">;</span></span>
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2119
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2293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2293" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2120
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2294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2294" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2295" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2296" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2297" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2298" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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2299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2299" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2300" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dmaxval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">NEGATIVE_INFINITY</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2301" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dminval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">POSITIVE_INFINITY</span><span class="o" style="font-weight: 600;">;</span></span>
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2302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2302" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2303" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2304" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2305" 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: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333333;">dmaxval</span><span class="o" style="font-weight: 600;">)</span></span>
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2306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2306" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2307" class="line" lang="java"> <span class="n" style="color: #333333;">dmaxval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">];</span></span>
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2308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2308" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2309" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2310" 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: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">dminval</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2311" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2312" class="line" lang="java"> <span class="n" style="color: #333333;">dminval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2313" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2314" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2315" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2316" 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: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2317" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2318" class="line" lang="java"> <span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">nstate</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333333;">nfile</span><span class="o" style="font-weight: 600;">]-</span><span class="n" style="color: #333333;">dminval</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333333;">dmaxval</span><span class="o" style="font-weight: 600;">;</span></span>
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2319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2319" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2320" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2321" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2121
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2322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2322" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2122
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2323
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2123
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2324
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2324" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">collabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2160" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2160,6 +2361,200 @@ public class StateAnalysis</td>
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2160
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<td class="new_line diff-line-num" data-linenumber="2361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2361
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2361" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2161
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<td class="new_line diff-line-num" data-linenumber="2362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2362
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2362" class="line" lang="java"> <span class="n" style="color: #333333;">makeEnrichmentHeatMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">heatmapfold</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">collabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">rowlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span></span>
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2162
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<td class="new_line diff-line-num" data-linenumber="2363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2363
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2363" class="line" lang="java"> <span class="s" style="color: #dd1144;">"Category"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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2364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2364" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2365" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2365" 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: #333333;">blogpvals</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2366" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2367" class="line" lang="java"> <span class="n" style="color: #333333;">makeEnrichmentHeatMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">heatmaplogpval</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">collabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">rowlabels</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">"_log10pvals"</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2368" class="line" lang="java"> <span class="s" style="color: #dd1144;">"Category"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #dd1144;">"State ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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2369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2369" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2370" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2371" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2372" class="line" lang="java"></span>
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2373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2373" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//////////////////////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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2374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2374" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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2375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2375" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> *this hashtable caches previously computed binomial coefficient values so they do not need to be recomputed</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2376" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2377" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2377" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #445588; font-weight: 600;">Hashtable</span> <span class="n" style="color: #333333;">htbinom</span> <span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">Hashtable</span><span class="o" style="font-weight: 600;">();</span></span>
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2378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2378" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2379" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2379" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2380" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2380" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Code based on STEM/DREM code I (Jason Ernst) previously wrote</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2381" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2381" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> *Returns the log of the binomial coefficient N choose ni</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2382" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2382" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2383" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2383" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">logbinomcoeff</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="no" style="color: #008080;">N</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2384" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2384" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2385" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2385" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">";"</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">N</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2386" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2386" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">Double</span> <span class="n" style="color: #333333;">dobj</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">htbinom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">sz</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2387" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2387" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">;</span></span>
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2388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2388" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2389" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2389" 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: #333333;">dobj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2390" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2390" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2391" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2391" class="line" lang="java"> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #445588; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333333;">dobj</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">doubleValue</span><span class="o" style="font-weight: 600;">();</span></span>
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2392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2392" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2393" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2394" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2394" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2395" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2395" class="line" lang="java"> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2396" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2396" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">dmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">,</span><span class="no" style="color: #008080;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2397" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2397" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">dmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">,</span><span class="no" style="color: #008080;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2398" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2398" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2399" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2399" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//the log of the part of the numerator not cancelled by </span></span>
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<td class="new_line diff-line-num new" data-linenumber="2400" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2400" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//the larger factorial in the denominator</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2401" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2401" 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: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dmax</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nj</span> <span class="o" style="font-weight: 600;"><=</span><span class="no" style="color: #008080;">N</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nj</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2402" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2402" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2403" class="line" lang="java"> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nj</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2404" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2405" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2405" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2406" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2406" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//subtract off the log of the denominator of the smaller term</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2407" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2407" 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: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nj</span> <span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333333;">dmin</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">nj</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2408" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2408" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2409" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2409" class="line" lang="java"> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nj</span><span class="o" style="font-weight: 600;">);</span></span>
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2410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2410" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2411" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2411" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//store it</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2412" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2412" class="line" lang="java"> <span class="n" style="color: #333333;">htbinom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">sz</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #445588; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">));</span></span>
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2413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2413" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2414" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2414" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2415" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2415" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">;</span></span>
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2416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2416" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2417" class="line" lang="java"></span>
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2418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2418" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2419" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2419" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//////////////////////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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2420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2420" class="line" lang="java"></span>
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2421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2421" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2422" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2422" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2423" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2423" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Code based on STEM/DREM code I (Jason Ernst) previously wrote</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2424" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2424" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Computes the probability of seeing more than nx successes in nN trials </span></span>
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2425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2425" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * where the probability of a success is dp.</span></span>
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2426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2426" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2427" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2427" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">binomialtail</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dp</span><span class="o" style="font-weight: 600;">)</span></span>
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2428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2428" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2429" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2429" 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: #333333;">nx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2430" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2430" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2431" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2431" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2432" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2432" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2433" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2433" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333333;">nx</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)||(</span><span class="n" style="color: #333333;">dp</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)||(</span><span class="n" style="color: #333333;">dp</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2434" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2434" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2435" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2435" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2436" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2436" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2437" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2437" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2438" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2438" class="line" lang="java"> <span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2439" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2439" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dterm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">logbinomcoeff</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2440" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2440" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dpv1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dp</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2441" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2441" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dpv2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dp</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2442" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2442" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2443" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2443" class="line" lang="java"> <span class="n" style="color: #333333;">dterm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dpv1</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333333;">dpv2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2444" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2444" class="line" lang="java"></span>
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2445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2445" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dterm</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2446" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2446" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dpdiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dpv1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dpv2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2447" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2447" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2448" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2448" 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: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">ni</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ni</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2449" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2449" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2450" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2450" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//N!/(ni!(N-ni)!)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2451" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2451" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//N!/((ni-1)!(N-ni+1)!)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2452" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2452" class="line" lang="java"> <span class="n" style="color: #333333;">dterm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nN</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">dpdiff</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2453" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2453" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2454" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2454" 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: #333333;">dterm</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2455" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2455" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2456" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2456
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2456" class="line" lang="java"> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dterm</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dterm</span><span class="o" style="font-weight: 600;">));</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2457" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2457
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2457" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2458" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2458" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2459" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2459
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2459" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2460" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2460
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2460" class="line" lang="java"> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dterm</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">));</span> </span>
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2461
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2461" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2462" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2462
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2462" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2463" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2463
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2463" class="line" lang="java"> <span class="n" style="color: #333333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2464" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2464
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2464" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2465" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2465
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2465" 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: #333333;">dprob</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2466" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2466
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2466" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2467" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2467
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2467" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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2468
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2468" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2469" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2469
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2469" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dprob</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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2470
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2470" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2471" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2471
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2471" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2472" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2472
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2472" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2473" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2473
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2473" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2474" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2474
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2474" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2475" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2475
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2475" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>
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2476
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2476" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2477
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2477" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2478
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2478" class="line" lang="java"></span>
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2479
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2480
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2480" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2481" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2481
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2481" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//////////////////////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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2482
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2482" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2483" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2483" class="line" lang="java"> <span class="cm" style="color: #999988; font-style: italic;">/**</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2484" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2484" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Code based on STEM/DREM code I (Jason Ernst) previously wrote</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2485" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2485" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * Returns the probability of seeing more than nx objects of type A, when there are nA objects of type A</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2486" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2486" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * nB objects of type B, and nm objects total drawn</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2487" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2487" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> * This can be used to compute a more accurate p-values than a 1-cumulative probability calculation</span></span>
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2488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2488" class="line" lang="java"><span class="cm" style="color: #999988; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2489" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2489" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="nf" style="color: #990000; font-weight: 600;">hypergeometrictail</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nA</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nB</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">)</span></span>
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2490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2490" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2491" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2491
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2491" 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: #333333;">nx</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2492" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2492
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2492" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2493
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2493" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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2494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2494" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2495" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2495" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2496" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2496
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2496" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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2497
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2497" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2498" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2498
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2498" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2499" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2499
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2499" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nminx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #999988; font-style: italic;">//the first element to the right of x or 0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2500" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2500
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2500" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">nmaxx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nA</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #999988; font-style: italic;">//the max of type A there can be </span></span>
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2501
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2501" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2502" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2502
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2502" 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: #333333;">nminx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333333;">nmaxx</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2503" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2503
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2503" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2504" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2504
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2504" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//if nx approaches infinity tail should be 0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2505" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2505
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2505" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2506" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2506
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2506" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2507" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2507" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2508" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2508" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">logbinomcoeff</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">nA</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">nB</span><span class="o" style="font-weight: 600;">)+</span> <span class="n" style="color: #333333;">logbinomcoeff</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nminx</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">nA</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2509" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2509
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2509" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">logbinomcoeff</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">nminx</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333333;">nB</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2510" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2510
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2510" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2511" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2511
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2511" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">double</span> <span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2512
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2512" 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: #445588; font-weight: 600;">long</span> <span class="n" style="color: #333333;">ni</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">nminx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ni</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333333;">nmaxx</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2513" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2513" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2514
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2514" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//computing the increase in probability mass</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2515
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2515" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//numerator has nA!/(ni!(nA-ni)!) * nB!/((nm-ni)!(nB-nm+ni)!)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2516
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2516" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//denominator has (nA+nB)!/(nm!(nA+nB-nm)!)</span></span>
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2517
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2517" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2518
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2518" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//numerator has nA!/((ni-1)!(nA-ni+1)!) * nB!/((nm-ni+1)!(nB-nm+ni-1)!)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2519" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2519
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2519" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//denominator has (nA+nB)!/(nm!(nA+nB-nm)!)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2520
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2520" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2521
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2521" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//cancelling gives</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2522
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2522" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//1/(ni!(nA-ni)!) * 1/((nm-ni)!(nB-nm+ni)!) over</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2523" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2523
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2523" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//1/((ni-1)!(nA-ni+1)!) * 1/((nm-ni+1)!(nB-nm+ni-1)!)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2524
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2524" class="line" lang="java"> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nA</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)-</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nB</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2525
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2525" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">nm</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)-</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">ni</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2526" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2527" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2527
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2527" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2528
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2528" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//log(a+b+c+d+e)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2529" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2529
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2529" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//log(e) + log(a+b+c+d+e) - log(e)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2530" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2530" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//log(e) + log((a+b+c+d+e)/e)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2531" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2531
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2531" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//log(e) + log(1+(a+b+c+d)/e)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2532
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2532" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//log(e) + log(1+Math.exp(log(a+b+c+d)-log(e)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2533" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2533
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2533" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2534" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2534
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2534" 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: #333333;">dsum</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2535
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2535" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2536" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2536
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2536" class="line" lang="java"> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dsum</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">));</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2537
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2537" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2538
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2538" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2539" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2539
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2539" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2540" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2540
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2540" class="line" lang="java"> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dlogprob</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">log</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dsum</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">));</span> </span>
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2541
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2541" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2542
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2542" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2543
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2543" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2544" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2544
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2544" class="line" lang="java"> <span class="n" style="color: #333333;">dprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">E</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333333;">dlogprob</span><span class="o" style="font-weight: 600;">);</span></span>
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2545
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2545" class="line" lang="java"></span>
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2546
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2546" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="2547" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2547
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2547" 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: #333333;">dprob</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2548" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2548
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2548" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2549" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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2550
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2550" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2551" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2551
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2551" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">dprob</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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2552
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2552" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2553" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2553
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2553" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #009999;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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2554
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2554" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2555
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2555" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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2556
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2556" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2557" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2557
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2557" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">dprob</span><span class="o" style="font-weight: 600;">;</span></span>
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2163
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2558
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2558" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2559
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2165
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2560
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2560" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2276,6 +2671,16 @@ public class StateAnalysis</td>
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2276
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<td class="new_line diff-line-num" data-linenumber="2671" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2671
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2671" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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2277
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2672
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2672" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2278
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2673
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2673" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2674" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2674
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2674" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2675" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2675
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2675" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2676" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2676
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2676" 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: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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2677
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2677" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2678" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2678
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2678" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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2679
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2679" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2680" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2680
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2680" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2681" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2681
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2681" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2682" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2682
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2682" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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2683
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2683" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2279
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<td class="new_line diff-line-num" data-linenumber="2684" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2684
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2684" class="line" lang="java"></span>
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2280
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<td class="new_line diff-line-num" data-linenumber="2685" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2685
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2685" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #999988; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>
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2281
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2686
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2686" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//an array of chromosome names</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2592,6 +2997,12 @@ public class StateAnalysis</td>
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2592
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<td class="new_line diff-line-num" data-linenumber="2997" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2997
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2997" 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: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2593" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2593
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<td class="new_line diff-line-num" data-linenumber="2998" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2998
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2998" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">szLineA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\\s+"</span><span class="o" style="font-weight: 600;">);</span></span>
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2594
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<td class="new_line diff-line-num" data-linenumber="2999" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2999
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2999" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2595" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3000" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3000
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3000" 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: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3001" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3001
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3001" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3002
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3002" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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3003
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3003" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLine</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" has "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" columns while expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">);</span></span>
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3004
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3004" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3005
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3005" class="line" lang="java"></span>
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2595
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<td class="new_line diff-line-num" data-linenumber="3006" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3006
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3006" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nchromindex</span><span class="o" style="font-weight: 600;">];</span> </span>
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2596
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<td class="new_line diff-line-num" data-linenumber="3007" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3007
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3007" 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: #333333;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szchromwant</span><span class="o" style="font-weight: 600;">))</span> </span>
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2597
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<td class="new_line diff-line-num" data-linenumber="3008" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3008
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3008" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2707" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2707,6 +3118,17 @@ public class StateAnalysis</td>
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2707
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<td class="new_line diff-line-num" data-linenumber="3118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3118
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3118" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="2708" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2708
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<td class="new_line diff-line-num" data-linenumber="3119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3119" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bstringlabels</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bbrowser</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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2709
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<td class="new_line diff-line-num" data-linenumber="3120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3120" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2710" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3121" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3122" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3123" 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: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3124" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3125" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3127" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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3128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3128" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3129" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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3130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3131" class="line" lang="java"></span>
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2710
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<td class="new_line diff-line-num" data-linenumber="3132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3132" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//highmem</span></span>
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<td class="old_line diff-line-num" data-linenumber="2711" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2711
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<td class="new_line diff-line-num" data-linenumber="3133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3133
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3133" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #999988; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>
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2712
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<td class="new_line diff-line-num" data-linenumber="3134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3134
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3134" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//stores all the segments in the data</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2935" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3357" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2935,9 +3357,15 @@ public class StateAnalysis</td>
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2935
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<td class="new_line diff-line-num" data-linenumber="3357" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3357
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3357" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333333;">brcoords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szanchorpositions</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2936" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2936
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<td class="new_line diff-line-num" data-linenumber="3358" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3358
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3358" 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: #333333;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">brcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</span><span class="o" style="font-weight: 600;">())!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2937" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2937
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<td class="new_line diff-line-num" data-linenumber="3359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3359
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3359" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2938" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2938
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<td class="new_line diff-line-num old" data-linenumber="3360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2938" class="line" lang="java"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2939" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3360" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3360" 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: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2939" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2939
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<td class="new_line diff-line-num" data-linenumber="3361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3361
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3361" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">szLineA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\\s+"</span><span class="o" style="font-weight: 600;">);</span></span>
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2940
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<td class="new_line diff-line-num" data-linenumber="3362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3362
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3362" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="2941" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3363" 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: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3364" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2941" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3365" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3365" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3366" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3366" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLine</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" has "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" columns while expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3367" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3367" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3368" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3368" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="2941" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2941
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<td class="new_line diff-line-num" data-linenumber="3369" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3369
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3369" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nchromindex</span><span class="o" style="font-weight: 600;">];</span> </span>
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<td class="old_line diff-line-num" data-linenumber="2942" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2942
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<td class="new_line diff-line-num" data-linenumber="3370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3370
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3370" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nanchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #445588; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">npositionindex</span><span class="o" style="font-weight: 600;">])-</span><span class="n" style="color: #333333;">noffsetanchor</span><span class="o" style="font-weight: 600;">);</span></span>
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2943
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<td class="new_line diff-line-num" data-linenumber="3371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3371
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3371" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bposstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3049" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3477" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3049,6 +3477,16 @@ public class StateAnalysis</td>
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3049
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<td class="new_line diff-line-num" data-linenumber="3477" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3477
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3477" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busestrand</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetanchor</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="3050" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3050
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<td class="new_line diff-line-num" data-linenumber="3478" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3478
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3478" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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3051
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<td class="new_line diff-line-num" data-linenumber="3479" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3479
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3479" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3052" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3480" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3480
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3480" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3052" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3481" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3481
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3481" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3482" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3482
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3482" 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: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3483" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3483" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3052" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3484" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3484" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3485" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3485" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3486" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3486" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3487" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3487" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3488" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3488" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3489" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3489" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3052
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<td class="new_line diff-line-num" data-linenumber="3490" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3490
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3490" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="3053" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3053
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<td class="new_line diff-line-num" data-linenumber="3491" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3491" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #999988; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>
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3054
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<td class="new_line diff-line-num" data-linenumber="3492" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3492
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3492" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//posterior here is really signal just using equivalent variable names</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3163" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3601" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3163,6 +3601,13 @@ public class StateAnalysis</td>
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3163
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<td class="new_line diff-line-num" data-linenumber="3601" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3601
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3601" 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: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3164" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3164
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<td class="new_line diff-line-num" data-linenumber="3602" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3602
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3602" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//going through all the coordinates keeping only those for the current chromosome</span></span>
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<td class="old_line diff-line-num" data-linenumber="3165" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3165
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<td class="new_line diff-line-num" data-linenumber="3603" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3603
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3603" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">szLineA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\\s+"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3604" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3604
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3604" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3605" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3605
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3605" 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: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3606" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3606
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3606" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3607" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3607
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3607" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3608" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3608
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3608" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLine</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" has "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" columns while expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">);</span></span>
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3609
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3609" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3610
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3610" class="line" lang="java"></span>
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3166
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<td class="new_line diff-line-num" data-linenumber="3611" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3611
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3611" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szreadchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nchromindex</span><span class="o" style="font-weight: 600;">];</span> </span>
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3167
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3612
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3612" class="line" lang="java"></span>
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3168
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3613
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3613" 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: #333333;">szreadchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3736" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3291,6 +3736,16 @@ public class StateAnalysis</td>
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3291
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<td class="new_line diff-line-num" data-linenumber="3736" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3736
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3736" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busestrand</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szcolfields</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">noffsetanchor</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="3292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3292
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<td class="new_line diff-line-num" data-linenumber="3737" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3737
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3737" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szoutfile</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">Color</span> <span class="n" style="color: #333333;">theColor</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">sztitle</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bprintimage</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #445588; font-weight: 600;">IOException</span></span>
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3293
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<td class="new_line diff-line-num" data-linenumber="3738" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3738
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3738" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3739" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3739
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3739" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3740" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3740
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3740" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">int</span> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #009999;">3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3741" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3741
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3741" 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: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3742" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3742
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3742" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3743" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3743
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3743" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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3744
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3744" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3745" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3745
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3745" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #990000; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333333;">busestrand</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333333;">busesignal</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3746" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3746
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3746" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3747" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3747
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3747" class="line" lang="java"> <span class="n" style="color: #333333;">nminnumcols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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3748
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3748" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3294
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3749
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3749" class="line" lang="java"></span>
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3295
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<td class="new_line diff-line-num" data-linenumber="3750" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3750
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3750" class="line" lang="java"> <span class="kt" style="color: #445588; font-weight: 600;">boolean</span> <span class="n" style="color: #333333;">bchrommatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="c1" style="color: #999988; font-style: italic;">//added in 1.23 to check for chromosome matches</span></span>
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3296
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<td class="new_line diff-line-num" data-linenumber="3751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3751" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//list of possible posterior files</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3403" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3858" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3403,6 +3858,14 @@ public class StateAnalysis</td>
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3403
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<td class="new_line diff-line-num" data-linenumber="3858" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3858
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3858" 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: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">""</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3404" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3404
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<td class="new_line diff-line-num" data-linenumber="3859" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3859
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3859" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//going through all the coordinates keeping only those for the current chromosome</span></span>
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3405
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<td class="new_line diff-line-num" data-linenumber="3860" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3860
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3860" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333333;">szLineA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"\\s+"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3861" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3861
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3861" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="3862" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3862
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3862" 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: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3863
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3863" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3864" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3864
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3864" class="line" lang="java"> <span class="c1" style="color: #999988; font-style: italic;">//v1.26</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3865" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3865
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3865" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #990000; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #dd1144;">"Line: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLine</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" in "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szanchorpositions</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" has "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #dd1144;">" columns while expecting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">nminnumcols</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3866" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3866
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3866" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3867
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3867" class="line" lang="java"></span>
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3868
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3868" class="line" lang="java"></span>
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3406
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<td class="new_line diff-line-num" data-linenumber="3869" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3869
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3869" class="line" lang="java"> <span class="nc" style="color: #445588; font-weight: 600;">String</span> <span class="n" style="color: #333333;">szreadchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">szLineA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333333;">theAnchorIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nchromindex</span><span class="o" style="font-weight: 600;">];</span> </span>
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3407
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3870
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3870" class="line" lang="java"></span>
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3408
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<td class="new_line diff-line-num" data-linenumber="3871" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3871
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3871" 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: #333333;">szreadchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/compare/cbe8d6b23a4ec662b3420d1933d7d1c22a720277...075ad1c2258313742856f695ee7e29d163cbda5b#6f75f608cf26f055e686012013a437ab1cfcdfed"><strong style="font-weight: 600;">versionlog.txt</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">1/2/2025 ChromHMM 1.26</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">* Added to ChromHMM's output -log10 p-values of enrichments when using OverlapEnrichment with the '-center' flag. This can be supressed with the use of the '-nopvals' flag</span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">* Fixed a bug when running OverlapEnrichment with the '-uniformscale' flag that caused ChromHMM to display an extraneous 'Genome %'</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">in the header row and 100% in the bottom row in the text file output. This did not effect the image files or running in a default mode without the flag.</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">* Fixed a bug when running OverlapEnrichment with the '-center' and '-multicount' flags that caused an incorrect base % for the annotation category</span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">to be reported.</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">* Provides a more informative error message when running NeighborhoodEnrichment and an input line has less than the expected number of entries</span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">* Now throws an error if the beginning of an output segment would be past the length of a chromosome specified in a file given with the "-l" option, which could be because a different assembly</span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">was used for the binarization.</span>
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext"></span>
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1
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext">12/28/2023 ChromHMM 1.25</span>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext">* Added the flag '-nobrowserheader' to LearnModel and MakeBrowserFiles to surpress the printing of header lines in browser bed files </span>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="plaintext">* Added the flag '-nopseudoinit' to LearnModel which prevents pseudocounts from being added in computing the emission parameter of the last mark and</span>
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