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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/jebl2">Debian Med / jebl2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jebl2/-/commit/b57cdf8e8222385ec3a1388d943603efcc5b13cb">b57cdf8e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-12T21:23:20+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.1+git20201011.969bd4b</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/jebl2/-/commit/fc8b5e70240df80a9daca55a403186e2258bff55">fc8b5e70</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-10-12T21:23:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.1+git20201011.969bd4b'
Update to upstream version '0.1+git20201011.969bd4b'
with Debian dir 8aee98082481852617590373f6d775240a8dc212</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jebl2/-/commit/2ea2a29a1068bab7a90bad6dd9b68a3d15a7273d">2ea2a29a</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-10-12T21:31:23+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/jebl2/-/commit/d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7">d0257dc5</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-10-12T21:31:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
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+
debian/upstream/metadata
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<li class="file-stats">
<a href="#cad7243bf7173c892a9443705670e4dc7ae381c9">
src/jebl/evolution/sequences/NucleotideState.java
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<li class="file-stats">
<a href="#7dfb22b1ab4dbe176a804746d979363b94388c48">
src/jebl/evolution/sequences/Nucleotides.java
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<li class="file-stats">
<a href="#b398c8795ceee664767f96c4ad99c1e619afede3">
src/jebl/evolution/sequences/State.java
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jebl2/-/compare/e38028b85ceebbf952ac782210b034ce983fabcb...d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">jebl2 (0.1+git20201011.969bd4b-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 0.1+git20201011.969bd4b</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Mon, 12 Oct 2020 21:24:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">jebl2 (0.1+git20200723.3a2ead5-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Pierre Gruet ]</span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/jebl2/-/compare/e38028b85ceebbf952ac782210b034ce983fabcb...d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Database: https://github.com/rambaut/jebl2/issues</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Submit: https://github.com/rambaut/jebl2/issues/new</span></pre>
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<li id="cad7243bf7173c892a9443705670e4dc7ae381c9">
<a href="https://salsa.debian.org/med-team/jebl2/-/compare/e38028b85ceebbf952ac782210b034ce983fabcb...d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7#cad7243bf7173c892a9443705670e4dc7ae381c9"><strong>src/jebl/evolution/sequences/NucleotideState.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,12 +16,14 @@ package jebl.evolution.sequences;</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">State</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">byte</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bitCode</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bitCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bitCode</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ambiguities</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">byte</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bitCode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ambiguities</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">stateCode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ambiguities</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bitCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bitCode</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"> <span class="nd">@Override</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,10 +33,17 @@ public final class NucleotideState extends State {</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">that</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">possiblyEqual</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">State</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bitCode</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">bitCode</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isGap</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Nucleotides</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">GAP_STATE</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceType</span> <span class="nf" style="color: #900; font-weight: 600;">getType</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">NUCLEOTIDE</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// a set of bits representing nucleotide states 0b0001 = A, 0b0010 = C, etc</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">bitCode</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="7dfb22b1ab4dbe176a804746d979363b94388c48">
<a href="https://salsa.debian.org/med-team/jebl2/-/compare/e38028b85ceebbf952ac782210b034ce983fabcb...d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7#7dfb22b1ab4dbe176a804746d979363b94388c48"><strong>src/jebl/evolution/sequences/Nucleotides.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,30 +28,40 @@ public final class Nucleotides {</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">CANONICAL_STATE_COUNT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">STATE_COUNT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">A_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Adenine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">C_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Cytosine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"C"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">G_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Guanine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"G"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">T_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Thymine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// The following line has been removed since it's never used and if it</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// was used would cause all sorts of bugs with various analysis code.</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// T_STATE represents either a U or a T depending on the context.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//public static final NucleotideState U_STATE = new NucleotideState("U", "U", 3);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">R_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">Y_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Y"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">M_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"M"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">W_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"W"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">S_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">K_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">B_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"B"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">D_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"D"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">11</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">H_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">12</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">V_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"V"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">N_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown base"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">14</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">UNKNOWN_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown base"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"?"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">GAP_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Gap"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">A_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Adenine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0001</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">C_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Cytosine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"C"</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0010</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">G_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Guanine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"G"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0100</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">T_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Thymine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1000</span><span class="o" style="font-weight: 600;">);</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// A: 0b0001 1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// C: 0b0010 2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// G: 0b0100 4</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// T: 0b1000 8</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// R: (byte)0b0101 5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Y: (byte)0b1010 10</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// M: (byte)0b0011 3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// W: (byte)0b1001 9</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// S: (byte)0b0110 6</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// K: (byte)0b1100 12</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// B: (byte)0b1110 14</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// D: (byte)0b1101 13</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// H: (byte)0b1011 11</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// V: (byte)0b0111 7</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">R_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0101</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">Y_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Y"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1010</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">M_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"M"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0011</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">W_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"W"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1001</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">S_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0110</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">K_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1100</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">B_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C/G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"B"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1110</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">D_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/G/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"D"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">11</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1101</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">H_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C/T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">12</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1011</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">V_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A/C/G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"V"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b0111</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">N_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown base"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">14</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1111</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">UNKNOWN_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown base"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"?"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1111</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span> <span class="no" style="color: #008080;">GAP_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Gap"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="mb">0b1111</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">NucleotideState</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="no" style="color: #008080;">A_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">C_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">G_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">T_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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55
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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"></span>
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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
56
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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Making an array public allows a client to modify its contents. Deprecating on 2007-10-10</span></span>
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57
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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and will become private in the future. Use {@link #getCanonicalStates} instead.</span></span>
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<a href="https://salsa.debian.org/med-team/jebl2/-/compare/e38028b85ceebbf952ac782210b034ce983fabcb...d0257dc5a1df1ba5e019525869ffa7a7b0fd32a7#b398c8795ceee664767f96c4ad99c1e619afede3"><strong>src/jebl/evolution/sequences/State.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,7 +68,7 @@ public abstract class State implements Comparable {</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param other another state to check for the quality with.</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param other another state to check for the <span class="idiff left right">e</span>quality with.</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return true if the other state is or possibly is equal to this state, taking ambiguities into account,</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * i.e. if the ambiguity sets of this and the other state intersect.</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,7 +99,7 @@ public abstract class State implements Comparable {</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Determine how much in common these potentially ambigous states have as a fraction between 0 and 1</span></span>
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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * 2 non-ambiguous states will return 0.</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * 2 identical non-ambig<span class="idiff left right">oues states will</span> 1.</span></span>
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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * 2 identical non-ambig<span class="idiff left right">uous states will return</span> 1.</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * e.g. for Nucleotides</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * R,A = 0.5</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * R,G = 0.5</span></span>
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