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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mauve-aligner">Debian Med / mauve-aligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203">b05e1390</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T22:43:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.0+4736</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f7a6d4ee5176fde95e2cd3204dedf32f5846de1f">
src/images/Back16.gif
</a>
</li>
<li class="file-stats">
<a href="#422d692db454ac94a3762120abae8c4a1c696003">
src/images/Down16.gif
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<li class="file-stats">
<a href="#479f8bc44dd1a2cd9b4479fc1a1cee3395849c95">
src/images/Forward16.gif
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<li class="file-stats">
<a href="#0d1155b41e3ac25071bbbc3a6cdc3c3c439e3e8e">
src/images/Home16.gif
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<li class="file-stats">
<a href="#837dffa144a09941b4114856cd5c180a6b88f066">
src/images/Up16.gif
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<li class="file-stats">
<a href="#fcfcdb61abcf83e44ead427292d029272905e735">
src/images/Zoom16.gif
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<li class="file-stats">
<a href="#7babfe1ede5c6d245e50f4f8f9af8183eb43c572">
src/images/ZoomIn16.gif
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<li class="file-stats">
<a href="#ecfd7d86b3c9b90949300d304d164f0625afe9e6">
src/images/ZoomIn24.gif
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<li class="file-stats">
<a href="#667e9f7ca92a8bd78d6ebfc41d7644f106ac45cc">
src/images/ZoomOut16.gif
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<li class="file-stats">
<a href="#6b3fd9737cb27706910e9742b9c5aae1cf820913">
src/images/ZoomOut24.gif
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<li class="file-stats">
<a href="#856beb75fe8cd06cc59c94c80ef93d71bfab0d49">
src/org/gel/mauve/analysis/SnpExporter.java
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<h4>Changes:</h4>
<li id="f7a6d4ee5176fde95e2cd3204dedf32f5846de1f">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#f7a6d4ee5176fde95e2cd3204dedf32f5846de1f"><strong>src/images/Back16.gif</strong></a>
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No preview for this file type
<br>
</li>
<li id="422d692db454ac94a3762120abae8c4a1c696003">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#422d692db454ac94a3762120abae8c4a1c696003"><strong>src/images/Down16.gif</strong></a>
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No preview for this file type
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</li>
<li id="479f8bc44dd1a2cd9b4479fc1a1cee3395849c95">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#479f8bc44dd1a2cd9b4479fc1a1cee3395849c95"><strong>src/images/Forward16.gif</strong></a>
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No preview for this file type
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</li>
<li id="0d1155b41e3ac25071bbbc3a6cdc3c3c439e3e8e">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#0d1155b41e3ac25071bbbc3a6cdc3c3c439e3e8e"><strong>src/images/Home16.gif</strong></a>
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No preview for this file type
<br>
</li>
<li id="837dffa144a09941b4114856cd5c180a6b88f066">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#837dffa144a09941b4114856cd5c180a6b88f066"><strong>src/images/Up16.gif</strong></a>
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<li id="fcfcdb61abcf83e44ead427292d029272905e735">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#fcfcdb61abcf83e44ead427292d029272905e735"><strong>src/images/Zoom16.gif</strong></a>
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No preview for this file type
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</li>
<li id="7babfe1ede5c6d245e50f4f8f9af8183eb43c572">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#7babfe1ede5c6d245e50f4f8f9af8183eb43c572"><strong>src/images/ZoomIn16.gif</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="ecfd7d86b3c9b90949300d304d164f0625afe9e6">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#ecfd7d86b3c9b90949300d304d164f0625afe9e6"><strong>src/images/ZoomIn24.gif</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="667e9f7ca92a8bd78d6ebfc41d7644f106ac45cc">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#667e9f7ca92a8bd78d6ebfc41d7644f106ac45cc"><strong>src/images/ZoomOut16.gif</strong></a>
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No preview for this file type
<br>
</li>
<li id="6b3fd9737cb27706910e9742b9c5aae1cf820913">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#6b3fd9737cb27706910e9742b9c5aae1cf820913"><strong>src/images/ZoomOut24.gif</strong></a>
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<br>
</li>
<li id="856beb75fe8cd06cc59c94c80ef93d71bfab0d49">
<a href="https://salsa.debian.org/med-team/mauve-aligner/commit/b05e1390083b83f9f57b1c704930a470f2964203#856beb75fe8cd06cc59c94c80ef93d71bfab0d49"><strong>src/org/gel/mauve/analysis/SnpExporter.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); 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="130" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -130,6 +130,7 @@ public class SnpExporter {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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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="LC130" 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;">snps</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>
</pre>
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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
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<td class="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">snps</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="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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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="LC132" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">flush</span><span class="o" style="font-weight: 600;">();</span> <span class="c1" style="color: #998; font-style: italic;">// don't forget to flush!</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
133
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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
134
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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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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="LC135" class="line" lang="java"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<pre style="margin: 0;"> <span id="LC136" 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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">exportGaps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">XmfaViewerModel</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">XMFAAlignment</span> <span class="n" style="color: #333;">xmfa</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">BufferedWriter</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,6 +140,7 @@ public class SnpExporter {</td>
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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<pre style="margin: 0;"> <span id="LC140" 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;">Gap</span><span class="o" style="font-weight: 600;">[]</span> <span class="nl">ar:</span> <span class="n" style="color: #333;">gaps</span><span class="o" style="font-weight: 600;">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
141
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<pre style="margin: 0;"> <span id="LC141" 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;">Gap</span> <span class="nl">g:</span> <span class="n" style="color: #333;">ar</span><span class="o" style="font-weight: 600;">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
141
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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
142
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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="LC142" class="line" lang="java"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">flush</span><span class="o" style="font-weight: 600;">();</span> <span class="c1" style="color: #998; font-style: italic;">// don't forget to flush!</span></span>
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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"> </span>
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144
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<pre style="margin: 0;"> <span id="LC146" 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;">SNP</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">getSNPs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">XmfaViewerModel</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">){</span></span>
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