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<h3>
Andreas Tille pushed to branch upstream
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/26097f2fc3174ef02f67d6625acf126203e196e6">26097f2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-05T12:14:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.1+git20180418.653eb83</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#bdc348bf75801c527f51cdeddc8edf027f7ef35a">
build.xml
</a>
</li>
<li class="file-stats">
<a href="#8111120ce373bc8027de3f5909a4816de84d10d8">
<span class="deleted-file">
−
lib/jam-mac-only.jar
</span>
</a>
</li>
<li class="file-stats">
<a href="#3a15ce6dbdf3d1d5ba1239a422cf2e01d5274f20">
src/jebl/evolution/io/NexusImporter.java
</a>
</li>
<li class="file-stats">
<a href="#3c3890dfe343b0902675ce9839d5dc11488ea7c4">
src/jebl/evolution/sequences/AminoAcids.java
</a>
</li>
<li class="file-stats">
<a href="#713576563e56ead17fb80a4e9ffaf16055241340">
src/jebl/evolution/sequences/Sequence.java
</a>
</li>
<li class="file-stats">
<a href="#71874bca010316b359bff06bc46f4d54d65f1336">
src/jebl/evolution/sequences/TranslatedSequence.java
</a>
</li>
<li class="file-stats">
<a href="#cf2a107ebe148c8452333edea6f66429db532dcd">
src/jebl/evolution/sequences/Utils.java
</a>
</li>
<li class="file-stats">
<a href="#c87dd915411af8a6f6779f7b10bbeea2058f0daa">
src/jebl/evolution/trees/RootedSubtree.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="bdc348bf75801c527f51cdeddc8edf027f7ef35a">
<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#bdc348bf75801c527f51cdeddc8edf027f7ef35a"><strong>build.xml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- set global properties for this build --></span></span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"src"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"src"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"build"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"build"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC10" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"build-mac-only"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"build-mac-only"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC12" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"lib"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"lib"</span><span class="nt" style="color: navy;">/></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"dist"</span><span class="nt" style="color: navy;">/></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">environment=</span><span class="s" style="color: #d14;">"env"</span><span class="nt" style="color: navy;">/></span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,31 +17,9 @@</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_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="xml"> <span class="nt" style="color: navy;"><tstamp/></span></span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the build directory structure used by compile --></span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(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="LC19" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build-mac-only}"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="xml"></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(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="LC26" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"compile-jam"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"init"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(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="LC27" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Compile the java code from ${jamsrc} into ${build} --></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="xml"> <span class="nt" style="color: navy;"><condition</span> <span class="na" style="color: teal;">property=</span><span class="s" style="color: #d14;">"isMac"</span><span class="nt" style="color: navy;">></span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="xml"> <span class="nt" style="color: navy;"><os</span> <span class="na" style="color: teal;">family=</span><span class="s" style="color: #d14;">"mac"</span><span class="nt" style="color: navy;">/></span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"></condition></span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="xml"> <span class="nt" style="color: navy;"><javac</span> <span class="na" style="color: teal;">source=</span><span class="s" style="color: #d14;">"1.5"</span> <span class="na" style="color: teal;">srcdir=</span><span class="s" style="color: #d14;">"${src}"</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"1.5"</span> <span class="na" style="color: teal;">destdir=</span><span class="s" style="color: #d14;">"${build}"</span> <span class="na" style="color: teal;">debug=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: navy;">></span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="xml"> <span class="nt" style="color: navy;"><include</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"org/**/*"</span><span class="nt" style="color: navy;">/></span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="xml"> <span class="nt" style="color: navy;"><exclude</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"org/**/maconly/*"</span> <span class="na" style="color: teal;">unless =</span> <span class="s" style="color: #d14;">"isMac"</span><span class="nt" style="color: navy;">/></span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="xml"> <span class="nt" style="color: navy;"></javac></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="xml"></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Utils.class was getting included in jebl.jar --></span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- twice and Pack200 was having issues. --></span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Doesn't seem to be the case for me, the class is missing! RM--></span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!--<delete file="${build}/org/virion/jam/mac/Utils.class"/>--></span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="xml"></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="xml"> <span class="nt" style="color: navy;"><copy</span> <span class="na" style="color: teal;">todir=</span><span class="s" style="color: #d14;">"${build}"</span><span class="nt" style="color: navy;">></span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${src}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"org/**/*.png"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="xml"> <span class="nt" style="color: navy;"></copy></span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="xml"></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"clean"</span><span class="nt" style="color: navy;">></span></span>
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48
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span><span class="nt" style="color: navy;">/></span></span>
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49
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="xml"> <span class="nt" style="color: navy;"><delete</span> <span class="na" style="color: teal;">includeEmptyDirs=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -52,41 +28,9 @@</td>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="xml"></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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54
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml"></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"compile-jam-mac-only"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"init"</span><span class="nt" style="color: navy;">></span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Compile the java code from ${jamsrc} into ${build} --></span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="xml"> <span class="nt" style="color: navy;"><condition</span> <span class="na" style="color: teal;">property=</span><span class="s" style="color: #d14;">"isMac"</span><span class="nt" style="color: navy;">></span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="xml"> <span class="nt" style="color: navy;"><os</span> <span class="na" style="color: teal;">family=</span><span class="s" style="color: #d14;">"mac"</span><span class="nt" style="color: navy;">/></span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="xml"> <span class="nt" style="color: navy;"></condition></span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="xml"> <span class="nt" style="color: navy;"><javac</span> <span class="na" style="color: teal;">source=</span><span class="s" style="color: #d14;">"1.5"</span> <span class="na" style="color: teal;">srcdir=</span><span class="s" style="color: #d14;">"${src}"</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"1.5"</span> <span class="na" style="color: teal;">destdir=</span><span class="s" style="color: #d14;">"${build-mac-only}"</span><span class="nt" style="color: navy;">></span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="xml"> <span class="nt" style="color: navy;"><include</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"org/**/maconly/*"</span><span class="nt" style="color: navy;">/></span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="xml"> <span class="nt" style="color: navy;"></javac></span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="xml"></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist-jam-mac-only"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"compile-jam-mac-only"</span> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"generate the -mac-only distribution"</span><span class="nt" style="color: navy;">></span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the distribution directory --></span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">/></span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="xml"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- create the mac-only jar file --></span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="xml"> <span class="nt" style="color: navy;"><jar</span> <span class="na" style="color: teal;">jarfile=</span><span class="s" style="color: #d14;">"${lib}/jam-mac-only.jar"</span><span class="nt" style="color: navy;">></span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build-mac-only}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/mac*/**/*.class,*.properties"</span><span class="nt" style="color: navy;">/></span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="xml"> <span class="nt" style="color: navy;"></jar></span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist-jam"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"compile-jam"</span> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"generate the JAM distribution"</span><span class="nt" style="color: navy;">></span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the distribution directory --></span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">/></span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="xml"> <span class="nt" style="color: navy;"><delete</span> <span class="na" style="color: teal;">file=</span><span class="s" style="color: #d14;">"${dist}/jam.jar"</span><span class="nt" style="color: navy;">/></span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Put everything in ${build} into the jam.jar file --></span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="xml"> <span class="nt" style="color: navy;"><jar</span> <span class="na" style="color: teal;">jarfile=</span><span class="s" style="color: #d14;">"${dist}/jam.jar"</span><span class="nt" style="color: navy;">></span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"org/**/*.class,org/**/*.properties,org/**/*.png"</span><span class="nt" style="color: navy;">/></span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="xml"> <span class="nt" style="color: navy;"><zipgroupfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${lib}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"jam-mac-only.jar"</span><span class="nt" style="color: navy;">/></span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="xml"> <span class="nt" style="color: navy;"></jar></span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"compile-jebl"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"init"</span><span class="nt" style="color: navy;">></span></span>
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88
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Compile the java code from ${src} into ${build} --></span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="xml"> <span class="nt" style="color: navy;"><javac</span> <span class="na" style="color: teal;">source=</span><span class="s" style="color: #d14;">"1.<span class="idiff left">5"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">srcdir=</span></span><span class="s" style="color: #d14;"><span class="idiff">"${src}"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">destdir=</span></span><span class="s" style="color: #d14;"><span class="idiff">"${build}"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">debug=</span></span><span class="s" style="color: #d14;"><span class="idiff">"true"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">target=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"1.5</span>"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="xml"> <span class="nt" style="color: navy;"><javac</span> <span class="na" style="color: teal;">source=</span><span class="s" style="color: #d14;">"1.<span class="idiff left">6"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">srcdir=</span></span><span class="s" style="color: #d14;"><span class="idiff">"${src}"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">destdir=</span></span><span class="s" style="color: #d14;"><span class="idiff">"${build}"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">debug=</span></span><span class="s" style="color: #d14;"><span class="idiff">"true"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">target=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"1.6</span>"</span><span class="nt" style="color: navy;">></span></span>
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90
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="xml"> <span class="nt" style="color: navy;"><include</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"jebl/**/*"</span><span class="nt" style="color: navy;">/></span></span>
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91
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="xml"> <span class="nt" style="color: navy;"></javac></span></span>
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92
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="xml"> <span class="nt" style="color: navy;"><copy</span> <span class="na" style="color: teal;">todir=</span><span class="s" style="color: #d14;">"${build}"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -101,32 +45,16 @@</td>
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101
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file --></span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="xml"> <span class="nt" style="color: navy;"><jar</span> <span class="na" style="color: teal;">jarfile=</span><span class="s" style="color: #d14;">"${dist}/jebl.jar"</span><span class="nt" style="color: navy;">></span></span>
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103
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"jebl/**/*.class,jebl/**/*.properties,jebl/**/*.png"</span><span class="nt" style="color: navy;">/></span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="xml"> <span class="nt" style="color: navy;"><zipgroupfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${lib}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/*.jar"</span><span class="nt" style="color: navy;">/></span></span>
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105
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml"> <span class="nt" style="color: navy;"></jar></span></span>
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106
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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107
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="xml"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"dist-jebl<span class="idiff left right">,dist-jam</span>"</span> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"generate the distribution"</span><span class="nt" style="color: navy;">></span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"dist-jebl"</span> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"generate the distribution"</span><span class="nt" style="color: navy;">></span></span>
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109
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the distribution directory --></span></span>
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110
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">/></span></span>
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111
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="xml"></span>
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112
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file --></span></span>
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113
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="xml"> <span class="nt" style="color: navy;"><jar</span> <span class="na" style="color: teal;">jarfile=</span><span class="s" style="color: #d14;">"${dist}/jebl.jar"</span><span class="nt" style="color: navy;">></span></span>
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114
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/*.class,**/*.properties,**/*.png"</span><span class="nt" style="color: navy;">/></span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="xml"> <span class="nt" style="color: navy;"><zipgroupfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${lib}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/*.jar"</span><span class="nt" style="color: navy;">/></span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="xml"> <span class="nt" style="color: navy;"></jar></span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="xml"></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"dist-clean"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"clean,compile-jebl,compile-jam"</span> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"generate the distribution"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- For some reason I don't fully understand, running the standard distribute</span></span>
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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> script doesn't always work if you have done a previous build on a previous version</span></span>
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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> of the source code. For some reason, it just doesn't compile some files. This</span></span>
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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> script seems to work better.--></span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file --></span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="xml"> <span class="nt" style="color: navy;"><jar</span> <span class="na" style="color: teal;">jarfile=</span><span class="s" style="color: #d14;">"${dist}/jebl.jar"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${build}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/*.class,**/*.properties,**/*.png"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="xml"> <span class="nt" style="color: navy;"><zipgroupfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${lib}"</span> <span class="na" style="color: teal;">includes=</span><span class="s" style="color: #d14;">"**/*.jar"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="xml"> <span class="nt" style="color: navy;"></jar></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="xml"></span>
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<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#8111120ce373bc8027de3f5909a4816de84d10d8"><strong>lib/jam-mac-only.jar</strong>
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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">@@ -1360,7 +1360,8 @@ public class NexusImporter implements AlignmentImporter, SequenceImporter, TreeI</td>
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// value=number, value="string", value={item1, item2, item3}</span></span>
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// (label must be quoted if it contains spaces (i.e. "my label"=label)</span></span>
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1362
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="java"></span>
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1363
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<pre style="margin: 0;">-<span id="LC1363" class="line" lang="java"> <span class="n" style="color: #333;">Pattern</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Pattern</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{[^=}]*\\}|\"[^\"]*\"+|[^,]+))?"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Pattern pattern = Pattern.compile("(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{[^=}]*\\}|\"[^\"]*\"+|[^,]+))?");</span></span>
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="java"> <span class="n" style="color: #333;">Pattern</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Pattern</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{(\\{[^\\}]+\\},?)+\\}|\\{[^\\}]+\\}|\"[^\"]*\"+|[^,]+))?"</span><span class="o" style="font-weight: 600;">);</span></span>
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1364
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1365
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="java"> <span class="n" style="color: #333;">Matcher</span> <span class="n" style="color: #333;">matcher</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">matcher</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">meta</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">matcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">find</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); 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="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1397,9 +1398,23 @@ public class NexusImporter implements AlignmentImporter, SequenceImporter, TreeI</td>
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1397
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="java"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">trim</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">startsWith</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="o" style="font-weight: 600;">{</span></span>
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1400
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the value is a list so recursively parse the elements</span></span>
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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and return an array</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="java"> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="java"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="java"></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="java"> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">elements</span><span class="o" style="font-weight: 600;">;</span></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="java"></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">startsWith</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="o" style="font-weight: 600;">{</span></span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the value is a list of a list so recursively parse the elements</span></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and return an array</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="java"></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// need to match },{ but leave the brackets in place</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="java"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">replaceAll</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="s" style="color: #d14;">"}@,@{"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="java"> <span class="n" style="color: #333;">elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"@,@"</span><span class="o" style="font-weight: 600;">);</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="java"></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the value is a list so recursively parse the elements</span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and return an array</span></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="java"> <span class="n" style="color: #333;">elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="java"> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">elements</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">elements</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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1405
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1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="java"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">elements</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#3c3890dfe343b0902675ce9839d5dc11488ea7c4"><strong>src/jebl/evolution/sequences/AminoAcids.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ public final class AminoAcids {</td>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">Z_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Glutamine or glutamic acid"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Glx"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Z"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">23</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">[]{</span><span class="n" style="color: #333;">E_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Q_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">J_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Leucine or Isoleucine"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Xle"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"J"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">24</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">[]{</span><span class="n" style="color: #333;">I_STATE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">L_STATE</span><span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">X_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown amino acid"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Xaa"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"X"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CANONICAL_STATES</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">UNKNOWN_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown amino acid"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Xaa"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">?</span>"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">26</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CANONICAL_STATES</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">UNKNOWN_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown amino acid"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Xaa"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">X</span>"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">26</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CANONICAL_STATES</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC75" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">STOP_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Stop codon"</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="s" style="color: #d14;">"*"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">27</span><span class="o" style="font-weight: 600;">);</span></span>
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76
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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AminoAcidState</span> <span class="n" style="color: #333;">GAP_STATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AminoAcidState</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="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">28</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CANONICAL_STATES</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// This really shouldn't include the canonical states, but I'm scared changing it may break stuff.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#713576563e56ead17fb80a4e9ffaf16055241340"><strong>src/jebl/evolution/sequences/Sequence.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">@@ -11,6 +11,11 @@ package jebl.evolution.sequences;</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.taxa.Taxon</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.util.Attributable</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collections</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * A biomolecular sequence.</span></span>
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<pre style="margin: 0;"> <span id="LC21" 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">@@ -21,20 +26,20 @@ import jebl.util.Attributable;</td>
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<pre style="margin: 0;"> <span id="LC26" 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="LC27" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">interface</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">Attributable</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Comparable</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the taxon that this sequence represents (primarily used to match sequences with tree nodes)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">Taxon</span> <span class="nf" style="color: #900; font-weight: 600;">getTaxon</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="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the taxon that this sequence represents (primarily used to match sequences with tree nodes)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">Taxon</span> <span class="nf" style="color: #900; font-weight: 600;">getTaxon</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the type of symbols that this sequence is made up of.</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">SequenceType</span> <span class="nf" style="color: #900; font-weight: 600;">getSequenceType</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="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the type of symbols that this sequence is made up of.</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">SequenceType</span> <span class="nf" style="color: #900; font-weight: 600;">getSequenceType</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return a string representing the sequence of symbols.</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getString</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="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return a string representing the sequence of symbols.</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getString</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return an array of state objects.</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">@@ -46,14 +51,71 @@ public interface Sequence extends Attributable, Comparable {</td>
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<pre style="margin: 0;"> <span id="LC51" 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="LC52" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">getStateIndices</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the state at site.</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">State</span> <span class="nf" style="color: #900; font-weight: 600;">getState</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;">site</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"><span class="idiff left right"> </span><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> * @return the state at site.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right"> </span> */</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"><span class="idiff left right"> </span><span class="n" style="color: #333;">State</span> <span class="nf" style="color: #900; font-weight: 600;">getState</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;">site</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Get the length of the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the length</span></span>
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<pre style="margin: 0;"> <span id="LC62" 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="LC58" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getLength</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getLength</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC65" 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="LC66" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Append two sequences together to create a new sequence object. New sequence has the taxon of</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the first sequence.</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sequence1</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sequence2</span></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;"> * @return</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;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Sequence</span> <span class="nf" style="color: #900; font-weight: 600;">appendSequences</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence2</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="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sequence2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sequences to be appended not of the same type"</span><span class="o" style="font-weight: 600;">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sequence2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">()];</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">(),</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">());</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">(),</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sequence2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">());</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">BasicSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getTaxon</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns a sub-sequence for states from, to (inclusive).</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sequence</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param from</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param to</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" 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="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Sequence</span> <span class="nf" style="color: #900; font-weight: 600;">getSubSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">from</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;">to</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"subsequence from is greater than to"</span><span class="o" style="font-weight: 600;">);</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLength</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"subsequence range out of bounds"</span><span class="o" style="font-weight: 600;">);</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">states</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">BasicSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getTaxon</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">);</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Sequence</span> <span class="nf" style="color: #900; font-weight: 600;">trimSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">trimStates</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="n" style="color: #333;">Set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trimSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashSet</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">asList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimStates</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="diff-line-num new new_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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sourceStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trimSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">BasicSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getTaxon</span><span class="o" style="font-weight: 600;">(),</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{}</span> <span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSubSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="n" style="color: #333;">sourceStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">();</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trimSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sourceStates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">getSubSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence1</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="71874bca010316b359bff06bc46f4d54d65f1336">
<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#71874bca010316b359bff06bc46f4d54d65f1336"><strong>src/jebl/evolution/sequences/TranslatedSequence.java</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">jebl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">evolution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author rambaut</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Date: Jul 27, 2005</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Time: 12:48:31 AM</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Andrew Rambaut</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TranslatedSequence</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">FilteredSequence</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Create a TranslatedSequence from a source codon or nucleotide sequence</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param source</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param geneticCode</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TranslatedSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">GeneticCode</span> <span class="n" style="color: #333;">geneticCode</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="LC14" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">geneticCode</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="LC15" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Create a TranslatedSequence from a source codon or nucleotide sequence</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param source</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param geneticCode</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param frame indexed from 1</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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="LC23" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TranslatedSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">GeneticCode</span> <span class="n" style="color: #333;">geneticCode</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;">frame</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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11
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<pre style="margin: 0;"> <span id="LC24" 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;">source</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>
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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: teal;">geneticCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geneticCode</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="n" style="color: #333;">State</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">filterSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">source</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="LC17" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">jebl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">evolution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">translate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">geneticCode</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">jebl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">evolution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">translate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">geneticCode</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">frame</span></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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"> <span class="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">@@ -25,5 +39,6 @@ public class TranslatedSequence extends FilteredSequence {</td>
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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;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">GeneticCode</span> <span class="n" style="color: #333;">geneticCode</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frame</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#cf2a107ebe148c8452333edea6f66429db532dcd"><strong>src/jebl/evolution/sequences/Utils.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">@@ -380,6 +380,28 @@ public class Utils {</td>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC382" 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="LC383" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Counts the number of stop codons in an amino acid sequence</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sequence the sequence string to count stop codons</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the number of stop codons</span></span>
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<pre style="margin: 0;">+<span id="LC386" 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="LC387" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getStopCodonCount</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="java"></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequenceType</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">SequenceType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">AMINO_ACID</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Sequence should be an amino acid sequence"</span><span class="o" style="font-weight: 600;">);</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="java"></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">State</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStates</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(((</span><span class="n" style="color: #333;">AminoAcidState</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">isStop</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="java"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">++;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="java"></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="java"></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="java"></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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383
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Produce a clean sequence filtered of spaces and digits.</span></span>
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384
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param seq the sequence</span></span>
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385
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param type the sequence type</span></span>
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<li id="c87dd915411af8a6f6779f7b10bbeea2058f0daa">
<a href="https://salsa.debian.org/med-team/jebl2/commit/26097f2fc3174ef02f67d6625acf126203e196e6#c87dd915411af8a6f6779f7b10bbeea2058f0daa"><strong>src/jebl/evolution/trees/RootedSubtree.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); 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="54" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -54,6 +54,12 @@ final public class RootedSubtree implements RootedTree {</td>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">children</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()</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>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"> <span class="n" style="color: #333;">newNode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createInternalNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">children</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Entry</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAttributeMap</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">entrySet</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;">newNode</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAttribute</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getKey</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getValue</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="n" style="color: #333;">setHeight</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newNode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeight</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">children</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="n" style="color: #333;">newNode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">children</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,17 +69,6 @@ final public class RootedSubtree implements RootedTree {</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newNode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// final Map<String, Object> map = node.getAttributeMap();</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if( ! map.isEmpty() ) {</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Entry</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAttributeMap</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">entrySet</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="n" style="color: #333;">newNode</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAttribute</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getKey</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getValue</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="n" style="color: #333;">setHeight</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newNode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeight</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newNode</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>
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