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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mafft">Debian Med / mafft</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f">e63b54a2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-02T18:59:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.490</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c08901e9ce7c420c65030b96053a390841b4a8cc">
core/Salignmm.c
</a>
</li>
<li class="file-stats">
<a href="#da6c9e8196ddbe34a06a7cbd5261fb01a8f536bc">
core/dvtditr.c
</a>
</li>
<li class="file-stats">
<a href="#bf392a27539c02d920458de76ae4ba00c5a3d6d0">
core/mafft.tmpl
</a>
</li>
<li class="file-stats">
<a href="#fb792f1c5a19dfe68974be08a96f0756ba949034">
core/mltaln.h
</a>
</li>
<li class="file-stats">
<a href="#d8fd3ccde311c1eafeb5d1cafe3579eb637d09d7">
core/mltaln9.c
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</li>
<li class="file-stats">
<a href="#dbcc9c77ee3546770696ba800e768f7e14b6d936">
core/tditeration.c
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<li class="file-stats">
<a href="#89c979518d42e3dfa78f14887a59dbd277a50c75">
core/treeOperation.c
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</li>
<li class="file-stats">
<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
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</li>
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<h4>Changes:</h4>
<li id="c08901e9ce7c420c65030b96053a390841b4a8cc">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f#c08901e9ce7c420c65030b96053a390841b4a8cc"><strong>core/Salignmm.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1208" 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">@@ -1208,7 +1208,6 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="c"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1209" 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="new_line diff-line-num" data-linenumber="1209" 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">
1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="c"> <span class="n" style="color: #333;">FreeFloatMtx</span><span class="p">(</span> <span class="n" style="color: #333;">doublework</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1210" 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">
1210
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<td class="new_line diff-line-num" data-linenumber="1210" 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">
1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c"> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">intwork</span> <span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1211" 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">
1211
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<td class="new_line diff-line-num old" data-linenumber="1211" 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="LC1211" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1212" 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">
1212
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<td class="new_line diff-line-num" data-linenumber="1211" 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">
1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1213" 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">
1213
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<td class="new_line diff-line-num" data-linenumber="1212" 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">
1212
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1212" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1214" 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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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1817" 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="1816" 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">@@ -1817,6 +1816,9 @@ for( i=0; i<lgth2; i++ )</td>
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<td class="old_line diff-line-num" data-linenumber="1817" 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">
1817
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<td class="new_line diff-line-num" data-linenumber="1816" 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">
1816
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1818" 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">
1818
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<td class="new_line diff-line-num" data-linenumber="1817" 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">
1817
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );</span></span>
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<td class="old_line diff-line-num" data-linenumber="1819" 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">
1819
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<td class="new_line diff-line-num" data-linenumber="1818" 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">
1818
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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chudanres</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1820" 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="new_line diff-line-num new" data-linenumber="1819" 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">
1819
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<pre style="margin: 0;">+<span id="LC1819" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1820" 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="new_line diff-line-num new" data-linenumber="1820" 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">
1820
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<pre style="margin: 0;">+<span id="LC1820" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mseq2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1821" 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">
1821
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<pre style="margin: 0;">+<span id="LC1821" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">mseq</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1820
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<td class="new_line diff-line-num" data-linenumber="1822" 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">
1822
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<pre style="margin: 0;"> <span id="LC1822" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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1821
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<td class="new_line diff-line-num" data-linenumber="1823" 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">
1823
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<pre style="margin: 0;"> <span id="LC1823" class="line" lang="c"> <span class="p">}</span></span>
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1822
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<td class="new_line diff-line-num" data-linenumber="1824" 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">
1824
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1900" 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="1902" 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">@@ -1900,6 +1902,9 @@ fprintf( stderr, "\n" );</td>
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1900
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1902
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<pre style="margin: 0;"> <span id="LC1902" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">chudanpt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chudanpt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">chudanref</span> <span class="p">)</span> </span>
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<td class="old_line diff-line-num" data-linenumber="1901" 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">
1901
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="c"> <span class="p">{</span></span>
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1902
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1904
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<pre style="margin: 0;"> <span id="LC1904" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );</span></span>
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1905
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<pre style="margin: 0;">+<span id="LC1905" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mseq2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1907
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<pre style="margin: 0;">+<span id="LC1907" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">mseq</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1903
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1908
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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chudanres</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1904
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1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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1910
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<pre style="margin: 0;"> <span id="LC1910" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f#da6c9e8196ddbe34a06a7cbd5261fb01a8f536bc"><strong>core/dvtditr.c</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">@@ -1139,15 +1139,27 @@ exit( 1 );</td>
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="c"></span>
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1140
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"done</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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1141
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span><span class="p">,</span> <span class="s" style="color: #d14;">"done</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span> <span class="p">);</span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">//</span> fclose( trap_g );<span class="idiff right"> // -> closeFiles()</span></span></span>
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1143
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="c"> <span class="n" style="color: #333;">freeconstants</span><span class="p">();</span></span>
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1144
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="c"></span>
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1145
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="c"></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="c"></span>
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1146
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="c"> <span class="n" style="color: #333;">devide</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </span>
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1147
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="c"> <span class="n" style="color: #333;">writePre</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">res_g</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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1148
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1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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1149
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> writeData( stdout, njob, name, nlen, res_g, 1 );</span></span>
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1150
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">nogap1seq</span> <span class="p">);</span></span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span> <span class="p">);</span></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="p">);</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">seq_g</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// seq_g_bk de free sareteirunode</span></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">res_g</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">aseq</span> <span class="p">);</span></span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">bseq</span> <span class="p">);</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">segment</span> <span class="p">);</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="c"> <span class="n" style="color: #333;">closeFiles</span><span class="p">();</span></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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1151
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1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="c"></span>
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1152
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1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="c"></span>
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1153
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">spscoreout</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"Unweighted sum-of-pairs score = %10.5f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">sumofpairsscore</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">res_g</span> <span class="p">)</span> <span class="p">);</span></span>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash </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="shell"><span class="nv" style="color: #008080;">er</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">myself</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span>/<span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>myself</span>
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4
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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.4<span class="idiff left">87</span> (2021/<span class="idiff right">Jul/25</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.4<span class="idiff left">90</span> (2021/<span class="idiff right">Oct/30</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">LANG</span><span class="o" style="font-weight: 600;">=</span>C<span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>LANG</span>
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6
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<td class="new_line diff-line-num" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">os</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</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">@@ -951,8 +951,12 @@ if [ $# -gt 0 ]; then</td>
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951
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># seektarget="-str"</span></span>
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952
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952
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--dash"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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953
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">newdash</span><span class="o" style="font-weight: 600;">=</span>1</span>
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954
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="shell"> <span class="nv" style="color: #008080;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"global"</span> <span class="c" style="color: #998; font-style: italic;"># can be override</span></span>
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955
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="shell"> <span class="nv" style="color: #008080;">iterate</span><span class="o" style="font-weight: 600;">=</span>3 <span class="c" style="color: #998; font-style: italic;"># can be override</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$distance</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"local"</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$distance</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"localgenaf"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># 2021/Oct</span></span>
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="shell"> <span class="nv" style="color: #008080;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"global"</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$iterate</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># 2021/Oct</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="shell"> <span class="nv" style="color: #008080;">iterate</span><span class="o" style="font-weight: 600;">=</span>3</span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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956
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="shell"><span class="k" style="font-weight: 600;"> elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--dashserver"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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957
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">shift</span></span>
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958
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">dashserver</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2358" 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="2362" 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">@@ -2358,7 +2362,8 @@ $ownlist"</td>
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2358
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2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$anysymbol</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2359
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2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mv </span>orig infile <span class="c" style="color: #998; font-style: italic;"># replaceu wo mukouka</span></span>
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2360
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2364
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<pre style="margin: 0;"> <span id="LC2364" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2361
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<pre style="margin: 0;">-<span id="LC2361" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/-//g'</span> infile <span class="o" style="font-weight: 600;">></span> dashin <span class="c" style="color: #998; font-style: italic;"># gap nozoku</span></span>
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># sed 's/-//g' infile > dashin # gap nozoku</span></span>
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<pre style="margin: 0;">+<span id="LC2366" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{if(/^>/)print; else {gsub( /-/,"" ); print;}}'</span> infile <span class="o" style="font-weight: 600;">></span> dashin</span>
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2367
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<pre style="margin: 0;"> <span id="LC2367" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2368" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;">-o</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC2369" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> 1>&2</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">@@ -36,7 +36,7 @@</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.4<span class="idiff left right">87</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.4<span class="idiff left right">90</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FFT_THRESHOLD 80</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">@@ -11278,6 +11278,7 @@ double DSPscore( int s, char **seq ) /* method 3 deha nai */</td>
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<pre style="margin: 0;"> <span id="LC11278" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC11279" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SEGMENTSIZE 150</span></span>
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<pre style="margin: 0;"> <span id="LC11280" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC11281" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC11282" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">searchAnchors</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">Segment</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seg</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11283" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC11284" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">kcyc</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11287" 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">@@ -11286,25 +11287,14 @@ int searchAnchors( int nseq, char **seq, Segment *seg )</td>
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<pre style="margin: 0;"> <span id="LC11287" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11288" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11289" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC11289" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stra</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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11290
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<pre style="margin: 0;">-<span id="LC11290" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11290" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stra</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11291" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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11292
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<pre style="margin: 0;">+<span id="LC11292" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">;</span></span>
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11293
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<pre style="margin: 0;"> <span id="LC11293" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cumscore</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC11292" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11294" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC11295" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC11295" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len</span> <span class="p">)</span></span>
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11296
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<pre style="margin: 0;">-<span id="LC11296" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC11297" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alloclen</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC11298" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC11299" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleVec</span><span class="p">(</span> <span class="n" style="color: #333;">stra</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC11300" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC11301" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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11302
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<pre style="margin: 0;">-<span id="LC11302" class="line" lang="c"> <span class="p">{</span></span>
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11303
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<pre style="margin: 0;">-<span id="LC11303" class="line" lang="c"> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">divThreshold</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">600</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divWinSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC11304" class="line" lang="c"> <span class="p">}</span></span>
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11305
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<pre style="margin: 0;">-<span id="LC11305" class="line" lang="c"> <span class="n" style="color: #333;">stra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleVec</span><span class="p">(</span> <span class="n" style="color: #333;">len</span> <span class="p">);</span></span>
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11306
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<pre style="margin: 0;">-<span id="LC11306" class="line" lang="c"> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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11307
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<pre style="margin: 0;">-<span id="LC11307" class="line" lang="c"> <span class="p">}</span></span>
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11296
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<pre style="margin: 0;">+<span id="LC11296" class="line" lang="c"> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">divThreshold</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">600</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">divWinSize</span><span class="p">;</span></span>
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11297
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<pre style="margin: 0;">+<span id="LC11297" class="line" lang="c"> <span class="n" style="color: #333;">stra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleVec</span><span class="p">(</span> <span class="n" style="color: #333;">len</span> <span class="p">);</span></span>
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11308
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11298
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<pre style="margin: 0;"> <span id="LC11298" class="line" lang="c"></span>
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11309
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11299
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<pre style="margin: 0;"> <span id="LC11299" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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11310
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11300
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<pre style="margin: 0;"> <span id="LC11300" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11372" 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">@@ -11382,6 +11372,8 @@ reporterr( "%d-%d length = %d\n", seg->start, seg->end, length );</td>
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11382
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11372
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<pre style="margin: 0;"> <span id="LC11372" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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11383
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11373
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<pre style="margin: 0;"> <span id="LC11373" class="line" lang="c"> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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11384
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11374
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<pre style="margin: 0;"> <span id="LC11374" class="line" lang="c"> <span class="p">}</span></span>
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11375
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<pre style="margin: 0;">+<span id="LC11375" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC11376" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleVec</span><span class="p">(</span> <span class="n" style="color: #333;">stra</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11377" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="n" style="color: #333;">value</span> <span class="p">);</span></span>
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11378
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<pre style="margin: 0;"> <span id="LC11378" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC11379" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f#dbcc9c77ee3546770696ba800e768f7e14b6d936"><strong>core/tditeration.c</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">@@ -269,11 +269,12 @@ static void freelocalarrays(</td>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">whichmtx</span></span>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"><span class="p">)</span></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"><span class="p">{</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "Skipping freelocalarrays\n" );</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// return;</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "freelocalarrays\n" );</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">commonIP</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">commonIP</span> <span class="p">);</span></span>
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276
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">commonIP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">commonAlloc1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">commonAlloc2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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277
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<td class="new_line diff-line-num" data-linenumber="278" 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">
278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">Falign</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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278
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<td class="new_line diff-line-num" data-linenumber="279" 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">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">Falign_localhom</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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279
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<td class="new_line diff-line-num" data-linenumber="280" 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">
280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">D__align</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1330" 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="1331" 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">@@ -1330,7 +1331,7 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],</td>
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1330
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1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="c"> <span class="n" style="color: #333;">Writeoptions</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span> <span class="p">);</span></span>
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1331
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span> <span class="p">);</span></span>
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1332
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<td class="new_line diff-line-num" data-linenumber="1333" 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">
1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="c"></span>
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1333
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<td class="new_line diff-line-num old" data-linenumber="1334" 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="LC1333" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">effarr</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* locnjob == njob ni kagiru */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1334" 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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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">effarr</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* locnjob == njob ni kagiru */</span></span>
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1334
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1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="c"> <span class="p">{</span></span>
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1335
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1336
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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="c"> <span class="n" style="color: #333;">indication1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharVec</span><span class="p">(</span> <span class="mi" style="color: #099;">150</span> <span class="p">);</span></span>
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1336
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<td class="new_line diff-line-num" data-linenumber="1337" 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">
1337
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="c"> <span class="n" style="color: #333;">indication2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharVec</span><span class="p">(</span> <span class="mi" style="color: #099;">150</span> <span class="p">);</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">@@ -2384,8 +2385,38 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],</td>
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2384
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2385
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2386
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="c"></span>
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2386
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2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="c"> <span class="nl">end:</span></span>
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<pre style="margin: 0;">-<span id="LC2387" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">grouprna1</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">grouprna1</span> <span class="p">);</span></span>
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2388
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<pre style="margin: 0;">-<span id="LC2388" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">grouprna2</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">grouprna2</span> <span class="p">);</span></span>
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2388
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( grouprna1 ) free( grouprna1 );</span></span>
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2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( grouprna2 ) free( grouprna2 );</span></span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="c"></span>
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2391
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2392
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="c"> <span class="n" style="color: #333;">freelocalarrays</span></span>
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2393
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="c"> <span class="p">(</span> </span>
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2394
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="c"> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="c"> <span class="n" style="color: #333;">grouprna1</span><span class="p">,</span> <span class="n" style="color: #333;">grouprna2</span><span class="p">,</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="c"> <span class="n" style="color: #333;">rnapairboth</span><span class="p">,</span></span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="c"> <span class="n" style="color: #333;">indication1</span><span class="p">,</span> <span class="n" style="color: #333;">indication2</span><span class="p">,</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="c"> <span class="n" style="color: #333;">distarr</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2399" 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">
2399
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="c"> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="c"> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="c"> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="c"> <span class="n" style="color: #333;">gapmap1</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap2</span><span class="p">,</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="c"> <span class="n" style="color: #333;">effarr1_kozo</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2_kozo</span><span class="p">,</span> <span class="n" style="color: #333;">effarr_kozo</span><span class="p">,</span></span>
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2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="c"> <span class="n" style="color: #333;">memlist</span><span class="p">,</span> <span class="n" style="color: #333;">pairbuf</span><span class="p">,</span></span>
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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="c"> <span class="n" style="color: #333;">localhomshrink</span><span class="p">,</span></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="c"> <span class="n" style="color: #333;">swaplist</span><span class="p">,</span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="c"> <span class="n" style="color: #333;">smalldistmtx</span><span class="p">,</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="c"> <span class="n" style="color: #333;">scoringmatrices</span><span class="p">,</span></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="c"> <span class="n" style="color: #333;">eff1s</span><span class="p">,</span> <span class="n" style="color: #333;">eff2s</span><span class="p">,</span></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="c"> <span class="n" style="color: #333;">whichmtx</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2411" 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">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="c"> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2412" 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">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">branchnode</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">branchnode</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2413" 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">
2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">stopol</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">stopol</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2414" 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">
2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mtx</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">mtx</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2415" 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">
2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">node</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">node</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2416" 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">
2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">branchWeight</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">branchWeight</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2417" 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">
2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">history</span><span class="p">)</span> <span class="n" style="color: #333;">FreeFloatCub</span><span class="p">(</span> <span class="n" style="color: #333;">history</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2418" 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">
2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="c"> <span class="n" style="color: #333;">treeCnv</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2021/Sep</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2419" 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">
2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2389
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2420
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<pre style="margin: 0;"> <span id="LC2420" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// freelocalarrays</span></span>
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2390
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2421
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<pre style="margin: 0;"> <span id="LC2421" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// ( </span></span>
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2391
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2422
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<pre style="margin: 0;"> <span id="LC2422" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// NULL,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2407" 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="2438" 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">@@ -2407,5 +2438,6 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],</td>
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2407
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2438
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<pre style="margin: 0;"> <span id="LC2438" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// );</span></span>
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2408
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2439
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<pre style="margin: 0;"> <span id="LC2439" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( branchnode );</span></span>
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2409
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2440
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<pre style="margin: 0;"> <span id="LC2440" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( stopol );</span></span>
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2441
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC2442" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="n" style="color: #333;">value</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2443" class="line" lang="c"><span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* int Tree... */</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f#89c979518d42e3dfa78f14887a59dbd277a50c75"><strong>core/treeOperation.c</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">@@ -129,14 +129,25 @@ void stopolInit( int n, Node *stopol )</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">treeCnv</span><span class="p">(</span> <span class="n" style="color: #333;">Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stopol</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">locnseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">bw</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">tmpintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">stopol</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">numintvec</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">tmpintvec</span><span class="p">[</span><span class="n" style="color: #333;">numintvec</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">tmpintvec</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">numintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">tmpintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">NodeInCub</span> <span class="n" style="color: #333;">parent</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ccount</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rep</span><span class="p">;</span></span>
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137
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmpint</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">tmpintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numintvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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140
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"></span>
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141
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">locnseq</span> <span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* oome */</span></span>
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142
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">count</span> <span class="p">)</span> <span class="n" style="color: #333;">ErrorExit</span><span class="p">(</span> <span class="s" style="color: #d14;">"Cannot allocate count.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f#f78a71af8bbf8cc2f6f313549d4da14bd3771359"><strong>readme</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> MAFFT: a multiple sequence alignment program</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.4<span class="idiff left">87</span>, 2021/<span class="idiff right">Jul/25</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.4<span class="idiff left">90</span>, 2021/<span class="idiff right">Oct/30</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> http://mafft.cbrc.jp/alignment/software/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> katoh@ifrec.osaka-u.ac.jp</span>
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