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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/82da29e9f1abd9a8a5798273dad78db14009d9da">82da29e9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-12T02:06:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.481</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#85e63b81c4a8412c5c397a27f8f12d6b8146fca9">
MPI/mltaln9_mpi.c
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<li class="file-stats">
<a href="#a1c64f77d2daf43174c04fc7fc3e44c15f3498d4">
core/blosum.c
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<li class="file-stats">
<a href="#26f0a508a6d1fe011e592f9175c2365c73e48e6e">
core/dash_client.go
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<li class="file-stats">
<a href="#58e2e0082bb4ca16bc55a2289e58d89f679360a0">
core/functions.h
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<li class="file-stats">
<a href="#258fa17aad7d901a96eadf2211f449a5e4eb2ef9">
core/io.c
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<li class="file-stats">
<a href="#bf392a27539c02d920458de76ae4ba00c5a3d6d0">
core/mafft.tmpl
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<li class="file-stats">
<a href="#fb792f1c5a19dfe68974be08a96f0756ba949034">
core/mltaln.h
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<li class="file-stats">
<a href="#d8fd3ccde311c1eafeb5d1cafe3579eb637d09d7">
core/mltaln9.c
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<li class="file-stats">
<a href="#d787ec50dfd9048f1124ca832aadca4ce7a4b51a">
core/tbfast.c
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<li class="file-stats">
<a href="#dbcc9c77ee3546770696ba800e768f7e14b6d936">
core/tditeration.c
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<li class="file-stats">
<a href="#5584b7e2129a1bb4aa5dabe72bb6a85d2efa2d9f">
core/univscript.tmpl
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<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
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<h4>Changes:</h4>
<li id="85e63b81c4a8412c5c397a27f8f12d6b8146fca9">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#85e63b81c4a8412c5c397a27f8f12d6b8146fca9"><strong>MPI/mltaln9_mpi.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mltaln.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <mpi.h></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef enableatomic</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdatomic.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" 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="12982" 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="12983" 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">@@ -12982,7 +12983,7 @@ void dontcalcimportance_firstone( int nseq, double *eff, char **seq, LocalHom **</td>
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12982
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12983
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<pre style="margin: 0;"> <span id="LC12983" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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12983
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12984
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<pre style="margin: 0;"> <span id="LC12984" class="line" lang="c"><span class="p">}</span></span>
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12984
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12985
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<pre style="margin: 0;"> <span id="LC12985" class="line" lang="c"></span>
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12985
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<pre style="margin: 0;">-<span id="LC12985" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12986" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">)</span></span>
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12987
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<pre style="margin: 0;"> <span id="LC12987" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC12988" 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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">tj</span><span class="p">;</span></span>
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12989
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<pre style="margin: 0;"> <span id="LC12989" 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;">importance</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</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">@@ -12991,7 +12992,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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12991
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<pre style="margin: 0;"> <span id="LC12992" 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;">nogaplen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</span></span>
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<pre style="margin: 0;"> <span id="LC12993" class="line" lang="c"> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpptr</span><span class="p">;</span></span>
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12994
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<pre style="margin: 0;"> <span id="LC12994" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC12994" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">nlenmax</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC12995" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">alloclen</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC12996" class="line" lang="c"> <span class="n" style="color: #333;">nogaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC12997" class="line" lang="c"> <span class="n" style="color: #333;">ieff</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;">nseq</span> <span class="p">);</span></span>
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12998
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<pre style="margin: 0;"> <span id="LC12998" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13026" 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">@@ -13025,7 +13026,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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13025
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13026
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<pre style="margin: 0;"> <span id="LC13026" class="line" lang="c"> <span class="p">{</span></span>
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13026
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13027
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<pre style="margin: 0;"> <span id="LC13027" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targetmapr</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">];</span></span>
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13028
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<pre style="margin: 0;"> <span id="LC13028" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "i = %d\n", i );</span></span>
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<pre style="margin: 0;">-<span id="LC13028" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">nlenmax</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13029" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">alloclen</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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13030
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<pre style="margin: 0;"> <span id="LC13030" class="line" lang="c"> <span class="n" style="color: #333;">importance</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</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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13031
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<pre style="margin: 0;"> <span id="LC13031" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nseq</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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13032
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<pre style="margin: 0;"> <span id="LC13032" class="line" lang="c"> <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">@@ -13048,7 +13049,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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13048
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13049
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<pre style="margin: 0;"> <span id="LC13049" class="line" lang="c"> <span class="p">}</span></span>
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13049
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13050
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<pre style="margin: 0;"> <span id="LC13050" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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13050
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13051
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<pre style="margin: 0;"> <span id="LC13051" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "position specific importance of seq %d:\n", i );</span></span>
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13051
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<pre style="margin: 0;">-<span id="LC13051" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">nlenmax</span>; pos++ )</span></span>
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13052
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<pre style="margin: 0;">+<span id="LC13052" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">alloclen</span>; pos++ )</span></span>
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13052
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13053
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<pre style="margin: 0;"> <span id="LC13053" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%d: %f\n", pos, importance[pos] );</span></span>
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13054
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<pre style="margin: 0;"> <span id="LC13054" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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13055
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<pre style="margin: 0;"> <span id="LC13055" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13216" 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">@@ -13215,7 +13216,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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13215
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13216
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<pre style="margin: 0;"> <span id="LC13216" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ieff</span> <span class="p">);</span></span>
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13216
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13217
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<pre style="margin: 0;"> <span id="LC13217" class="line" lang="c"><span class="p">}</span></span>
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13218
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<pre style="margin: 0;"> <span id="LC13218" class="line" lang="c"></span>
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13218
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<pre style="margin: 0;">-<span id="LC13218" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">)</span></span>
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13219
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<pre style="margin: 0;">+<span id="LC13219" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">)</span></span>
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13220
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<pre style="margin: 0;"> <span id="LC13220" class="line" lang="c"><span class="p">{</span></span>
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13220
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13221
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<pre style="margin: 0;"> <span id="LC13221" 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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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13221
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13222
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<pre style="margin: 0;"> <span id="LC13222" 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;">importance</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13224" 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="13225" 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">@@ -13224,7 +13225,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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13224
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13225
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<pre style="margin: 0;"> <span id="LC13225" 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;">nogaplen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</span></span>
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13225
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13226
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<pre style="margin: 0;"> <span id="LC13226" class="line" lang="c"> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpptr</span><span class="p">;</span></span>
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13226
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13227
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<pre style="margin: 0;"> <span id="LC13227" class="line" lang="c"></span>
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13227
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<pre style="margin: 0;">-<span id="LC13227" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">nlenmax</span></span> <span class="p">);</span></span>
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13228
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<pre style="margin: 0;">+<span id="LC13228" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">alloclen</span></span> <span class="p">);</span></span>
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13228
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13229
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<pre style="margin: 0;"> <span id="LC13229" class="line" lang="c"> <span class="n" style="color: #333;">nogaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="p">);</span></span>
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13229
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13230
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<pre style="margin: 0;"> <span id="LC13230" class="line" lang="c"> <span class="n" style="color: #333;">ieff</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;">nseq</span> <span class="p">);</span></span>
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13230
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13231
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<pre style="margin: 0;"> <span id="LC13231" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13256" 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="13257" 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">@@ -13256,7 +13257,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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13256
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13257
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<pre style="margin: 0;"> <span id="LC13257" 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;">nseq</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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13257
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13258
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<pre style="margin: 0;"> <span id="LC13258" class="line" lang="c"> <span class="p">{</span></span>
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13258
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13259
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<pre style="margin: 0;"> <span id="LC13259" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "i = %d\n", i );</span></span>
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13259
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<pre style="margin: 0;">-<span id="LC13259" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">nlenmax</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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13260
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<pre style="margin: 0;">+<span id="LC13260" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">alloclen</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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13260
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13261
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<pre style="margin: 0;"> <span id="LC13261" class="line" lang="c"> <span class="n" style="color: #333;">importance</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</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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13261
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13262
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<pre style="margin: 0;"> <span id="LC13262" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nseq</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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13262
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13263
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<pre style="margin: 0;"> <span id="LC13263" 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="13300" 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">@@ -13299,7 +13300,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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13299
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13300
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<pre style="margin: 0;"> <span id="LC13300" class="line" lang="c"> <span class="p">}</span></span>
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13300
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13301
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<pre style="margin: 0;"> <span id="LC13301" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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13301
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13302
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<pre style="margin: 0;"> <span id="LC13302" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "position specific importance of seq %d:\n", i );</span></span>
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13302
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<pre style="margin: 0;">-<span id="LC13302" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">nlenmax</span>; pos++ )</span></span>
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13303
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<pre style="margin: 0;">+<span id="LC13303" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">alloclen</span>; pos++ )</span></span>
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13303
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13304
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<pre style="margin: 0;"> <span id="LC13304" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%d: %f\n", pos, importance[pos] );</span></span>
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13304
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13305
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<pre style="margin: 0;"> <span id="LC13305" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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13305
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13306
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<pre style="margin: 0;"> <span id="LC13306" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#a1c64f77d2daf43174c04fc7fc3e44c15f3498d4"><strong>core/blosum.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" 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="397" 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">@@ -397,6 +397,7 @@ static void overridematrix( double **matrix )</td>
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397
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">][</span><span class="n" style="color: #333;">i2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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398
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">][</span><span class="n" style="color: #333;">i1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 2018/May/11</span></span>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span> <span class="n" style="color: #333;">fp</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">extendedmtx</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;">matrix</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;">freq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">amino</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;">amino_grp</span> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#26f0a508a6d1fe011e592f9175c2365c73e48e6e"><strong>core/dash_client.go</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">@@ -20,7 +20,7 @@ var VersionNumber = 1.1</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">Debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">false</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">NumberOfQueryTries</span> <span class="o" style="font-weight: 600;">=</span> <span class="m" style="color: #099;">12</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">HTTPClient</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">http</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Client</span><span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">SequenceLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="m" style="color: #099;"><span class="idiff left right">75</span>0</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">SequenceLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="m" style="color: #099;"><span class="idiff left right">300</span>0</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">AlignmentLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="m" style="color: #099;">10000</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">//URL's</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#58e2e0082bb4ca16bc55a2289e58d89f679360a0"><strong>core/functions.h</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">@@ -62,12 +62,12 @@ extern int searchAnchors( int nseq, char **seq, Segment *seg );</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">progName</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;">str</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dontcalcimportance</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dontcalcimportance_target</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ntarget</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dontcalcimportance_lastone</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dontcalcimportance_firstone</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dontcalcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">weightimportance2</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</span><span class="p">,</span> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">weightimportance4</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clus2</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;">eff1</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;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">extendlocalhom</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="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#258fa17aad7d901a96eadf2211f449a5e4eb2ef9"><strong>core/io.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="432" 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">@@ -432,7 +432,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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432
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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433
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="c"> <span class="p">{</span></span>
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434
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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="LC436" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"> <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">@@ -489,7 +492,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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="LC496" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"> <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">@@ -516,7 +522,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subnosento</span><span class="p">;</span> <span class="n" style="color: #333;">tmppt</span><span class="p">;</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumoverlap</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumscore</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sumoverlap</span><span class="p">;</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumscore</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sumoverlap</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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520
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529
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<pre style="margin: 0;"> <span id="LC529" 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;">"tmpptr->opt = %f</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;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"> <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">@@ -568,7 +577,10 @@ void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int</td>
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="c"> <span class="p">{</span></span>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <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">@@ -623,7 +635,10 @@ void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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<pre style="margin: 0;">-<span id="LC626" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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="LC639" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="c"> <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">@@ -755,7 +770,10 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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<pre style="margin: 0;">-<span id="LC758" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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="LC774" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="c"> <span class="p">}</span></span>
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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779
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<pre style="margin: 0;"> <span id="LC779" 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="830" 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">@@ -812,7 +830,10 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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812
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">divpairscore</span> <span class="p">)</span></span>
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813
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="c"> <span class="p">{</span></span>
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start2</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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815
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">600</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="c"> <span class="p">}</span></span>
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817
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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839
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<pre style="margin: 0;"> <span id="LC839" 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="857" 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">@@ -836,8 +857,11 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off</td>
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836
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localhompt</span><span class="p">;</span> <span class="n" style="color: #333;">tmppt</span><span class="p">;</span> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="p">)</span></span>
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837
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="c"> <span class="p">{</span></span>
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838
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumoverlap</span><span class="p">;</span></span>
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839
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">isumscore</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span> <span class="mi" style="color: #099;">600</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sumoverlap</span> <span class="p">);</span></span>
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840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapaa</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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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">isumscore</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span> <span class="mi" style="color: #099;">600</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sumoverlap</span> <span class="p">);</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="n" style="color: #333;">tmppt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "tmpptr->opt = %f, sumoverlap=%d\n", tmppt->opt, sumoverlap );</span></span>
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841
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="c"> <span class="p">}</span></span>
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842
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="c"> <span class="p">}</span></span>
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843
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="c"><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">75</span> (202<span class="idiff">0/Nov</span>/2<span class="idiff right">3</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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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">81</span> (202<span class="idiff">1/May</span>/2<span class="idiff right">6</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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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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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">@@ -1034,7 +1034,7 @@ if [ $# -gt 0 ]; then</td>
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1034
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TMPFILE</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>cygpath <span class="nt" style="color: #000080;">-w</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span> <span class="c" style="color: #998; font-style: italic;"># necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.</span></span>
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1035
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1036
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="shell"></span>
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1037
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<pre style="margin: 0;">-<span id="LC1037" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">umask </span>077</span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left">#</span> umask 077<span class="idiff right"> # 2021/Jan</span></span></span>
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1038
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mkdir "$TMPFILE" || er=1</span></span>
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1039
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="shell"></span>
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1040
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2373" 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="2373" 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">@@ -2373,7 +2373,7 @@ $ownlist"</td>
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2373
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2373
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<pre style="margin: 0;"> <span id="LC2373" class="line" lang="shell"> <span class="nv" style="color: #008080;">dashres</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$?</span><span class="s2" style="color: #d14;">"</span></span>
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2374
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2374
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<pre style="margin: 0;"> <span id="LC2374" 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;">$dashres</span> <span class="nt" style="color: #000080;">-ne</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2375
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2375
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<pre style="margin: 0;"> <span id="LC2375" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Error in DASH"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2376
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<pre style="margin: 0;">-<span id="LC2376" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"To <span class="idiff left">us</span>e this feature, compile<span class="idiff right">d</span> with"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2376
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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"To <span class="idiff left">enabl</span>e this feature, compile with<span class="idiff right"> DASH_CLIENT=dash_client. Go compiler is necessary.</span>"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2377
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2377
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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
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2378
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2378
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<pre style="margin: 0;"> <span id="LC2378" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2379
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2379
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<pre style="margin: 0;"> <span id="LC2379" class="line" lang="shell"></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">@@ -2945,8 +2945,8 @@ BEGIN {</td>
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2945
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2945
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<pre style="margin: 0;"> <span id="LC2945" class="line" lang="shell"><span class="s1" style="color: #d14;"> while( 1 )</span></span>
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2946
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2946
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<pre style="margin: 0;"> <span id="LC2946" class="line" lang="shell"><span class="s1" style="color: #d14;"> {</span></span>
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2947
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2947
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<pre style="margin: 0;"> <span id="LC2947" class="line" lang="shell"><span class="s1" style="color: #d14;"> go = 0;</span></span>
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2948
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<pre style="margin: 0;">-<span id="LC2948" class="line" lang="shell"><span class="s1" style="color: #d14;"> printf( "<span class="idiff left right">OK?</span>\n" ) > "/dev/tty";</span></span>
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<pre style="margin: 0;">-<span id="LC2949" class="line" lang="shell"><span class="s1" style="color: #d14;"> printf( "@ <span class="idiff left right">[Y] </span>" ) > "/dev/tty";</span></span>
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<pre style="margin: 0;">+<span id="LC2948" class="line" lang="shell"><span class="s1" style="color: #d14;"> printf( "<span class="idiff left right">Type Y or just enter to run this command.</span>\n" ) > "/dev/tty";</span></span>
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<pre style="margin: 0;">+<span id="LC2949" class="line" lang="shell"><span class="s1" style="color: #d14;"> printf( "@ " ) > "/dev/tty";</span></span>
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<pre style="margin: 0;"> <span id="LC2950" class="line" lang="shell"><span class="s1" style="color: #d14;"> res = getline < "/dev/tty";</span></span>
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<pre style="margin: 0;"> <span id="LC2951" class="line" lang="shell"><span class="s1" style="color: #d14;"> close( "/dev/tty" );</span></span>
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<pre style="margin: 0;"> <span id="LC2952" class="line" lang="shell"><span class="s1" style="color: #d14;"> if( res == 0 )</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">@@ -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="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.4<span class="idiff left right">75</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">81</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">@@ -11528,7 +11528,7 @@ void dontcalcimportance_firstone( int nseq, double *eff, char **seq, LocalHom **</td>
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<pre style="margin: 0;"> <span id="LC11528" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC11529" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC11530" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC11531" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11531" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_target</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;">int</span> <span class="n" style="color: #333;">ntarget</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;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</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;">targetmap</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;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">)</span></span>
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11532
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<pre style="margin: 0;"> <span id="LC11532" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC11533" 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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">tj</span><span class="p">;</span></span>
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11534
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<pre style="margin: 0;"> <span id="LC11534" 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;">importance</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</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">@@ -11537,7 +11537,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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11537
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11537
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<pre style="margin: 0;"> <span id="LC11537" 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;">nogaplen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</span></span>
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11538
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<pre style="margin: 0;"> <span id="LC11538" class="line" lang="c"> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpptr</span><span class="p">;</span></span>
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11539
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11539
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<pre style="margin: 0;"> <span id="LC11539" class="line" lang="c"></span>
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11540
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<pre style="margin: 0;">-<span id="LC11540" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">nlenmax</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC11540" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;"><span class="idiff left right">alloclen</span></span> <span class="p">);</span></span>
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11541
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<pre style="margin: 0;"> <span id="LC11541" class="line" lang="c"> <span class="n" style="color: #333;">nogaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11542" class="line" lang="c"> <span class="n" style="color: #333;">ieff</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;">nseq</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11543" class="line" lang="c"></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">@@ -11571,7 +11571,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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11571
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11571
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<pre style="margin: 0;"> <span id="LC11571" class="line" lang="c"> <span class="p">{</span></span>
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11572
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11572
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<pre style="margin: 0;"> <span id="LC11572" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targetmapr</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">];</span></span>
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11573
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11573
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<pre style="margin: 0;"> <span id="LC11573" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "i = %d\n", i );</span></span>
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11574
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<pre style="margin: 0;">-<span id="LC11574" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">nlenmax</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11574" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">alloclen</span></span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11575" class="line" lang="c"> <span class="n" style="color: #333;">importance</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</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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11576
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<pre style="margin: 0;"> <span id="LC11576" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nseq</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11577" class="line" lang="c"> <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">@@ -11594,7 +11594,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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<pre style="margin: 0;"> <span id="LC11594" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC11595" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<pre style="margin: 0;"> <span id="LC11596" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "position specific importance of seq %d:\n", i );</span></span>
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<pre style="margin: 0;">-<span id="LC11597" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">nlenmax</span>; pos++ )</span></span>
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<pre style="margin: 0;">+<span id="LC11597" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( pos=0; pos<<span class="idiff left right">alloclen</span>; pos++ )</span></span>
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<pre style="margin: 0;"> <span id="LC11598" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%d: %f\n", pos, importance[pos] );</span></span>
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<pre style="margin: 0;"> <span id="LC11599" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<pre style="margin: 0;"> <span id="LC11600" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</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">@@ -11761,7 +11761,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca</td>
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11761
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<pre style="margin: 0;"> <span id="LC11761" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ieff</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11762" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC11763" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC11764" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11764" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calcimportance_half</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;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</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;">LocalHom</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">localhom</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11765" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC11766" 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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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11767
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<pre style="margin: 0;"> <span id="LC11767" 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;">importance</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</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">@@ -11770,7 +11770,8 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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11770
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11770
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<pre style="margin: 0;"> <span id="LC11770" 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;">nogaplen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// static -> local, 2012/02/25</span></span>
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11771
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<pre style="margin: 0;"> <span id="LC11771" class="line" lang="c"> <span class="n" style="color: #333;">LocalHom</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpptr</span><span class="p">;</span></span>
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11772
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<pre style="margin: 0;"> <span id="LC11772" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC11773" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;">nlenmax</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC11773" class="line" lang="c"> <span class="n" style="color: #333;">importance</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;">alloclen</span> <span class="p">);</span></span>
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11774
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<pre style="margin: 0;">+<span id="LC11774" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr("alloclen=%d, nlenmax=%d\n", alloclen, nlenmax );</span></span>
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11774
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11775
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<pre style="margin: 0;"> <span id="LC11775" class="line" lang="c"> <span class="n" style="color: #333;">nogaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="p">);</span></span>
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11775
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11776
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<pre style="margin: 0;"> <span id="LC11776" class="line" lang="c"> <span class="n" style="color: #333;">ieff</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;">nseq</span> <span class="p">);</span></span>
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11777
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<pre style="margin: 0;"> <span id="LC11777" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11802" 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="11803" 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">@@ -11802,8 +11803,10 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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11802
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11803
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<pre style="margin: 0;"> <span id="LC11803" 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;">nseq</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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11803
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11804
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<pre style="margin: 0;"> <span id="LC11804" class="line" lang="c"> <span class="p">{</span></span>
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11804
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11805
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<pre style="margin: 0;"> <span id="LC11805" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "i = %d\n", i );</span></span>
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11805
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<pre style="margin: 0;">-<span id="LC11805" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nlenmax</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11806" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alloclen</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11807" class="line" lang="c"> <span class="p">{</span></span>
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11808
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<pre style="margin: 0;"> <span id="LC11808" class="line" lang="c"> <span class="n" style="color: #333;">importance</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</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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<pre style="margin: 0;">+<span id="LC11809" class="line" lang="c"> <span class="p">}</span></span>
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11807
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11810
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<pre style="margin: 0;"> <span id="LC11810" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nseq</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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11808
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11811
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<pre style="margin: 0;"> <span id="LC11811" class="line" lang="c"> <span class="p">{</span></span>
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11809
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11812
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<pre style="margin: 0;"> <span id="LC11812" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">j</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11815" 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">@@ -11812,6 +11815,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom</td>
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11812
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11815
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<pre style="margin: 0;"> <span id="LC11815" class="line" lang="c"> <span class="p">{</span></span>
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11813
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11816
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<pre style="margin: 0;"> <span id="LC11816" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">tmpptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localhom</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">tmpptr</span><span class="p">;</span> <span class="n" style="color: #333;">tmpptr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmpptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="p">)</span></span>
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11814
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11817
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<pre style="margin: 0;"> <span id="LC11817" class="line" lang="c"> <span class="p">{</span></span>
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11818
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<pre style="margin: 0;">+<span id="LC11818" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "pos=%d, alloclen=%d\n", pos, alloclen );</span></span>
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11815
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11819
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<pre style="margin: 0;"> <span id="LC11819" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmpptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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11816
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11820
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<pre style="margin: 0;"> <span id="LC11820" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmpptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start1</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">tmpptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end1</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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11821
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<pre style="margin: 0;"> <span id="LC11821" class="line" lang="c"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#d787ec50dfd9048f1124ca832aadca4ce7a4b51a"><strong>core/tbfast.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1337,10 +1337,10 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq</td>
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1337
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1337
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">constraint</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compacttree</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span> <span class="p">)</span></span>
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="c"> <span class="p">{</span></span>
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1339
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1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specifictarget</span> <span class="p">)</span></span>
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1340
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<pre style="margin: 0;">-<span id="LC1340" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span> <span class="p">);</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dontcalcimportance_target( njob, effarr, aseq, localhomtable, ntarget ); //CHUUI</span></span>
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1343
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span> <span class="p">);</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dontcalcimportance_half( njob, effarr, aseq, localhomtable ); //CHUUI</span></span>
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1345
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="c"> <span class="p">}</span></span>
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1346
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">constraint</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nseed</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// ie, compacttree == 3 && constraint > 0 </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3320" 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="3320" 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">@@ -3320,10 +3320,10 @@ int main( int argc, char *argv[] )</td>
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<pre style="margin: 0;"> <span id="LC3320" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">constraint</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compacttree</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC3321" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3322" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specifictarget</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3323" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">eff</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3323" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">eff</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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3324
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<pre style="margin: 0;"> <span id="LC3324" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dontcalcimportance_target( njob, eff, bseq, localhomtable, ntarget ); // CHUUI</span></span>
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3325
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3325
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<pre style="margin: 0;"> <span id="LC3325" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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3326
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<pre style="margin: 0;">-<span id="LC3326" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">eff</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span> <span class="p">);</span></span>
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3326
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<pre style="margin: 0;">+<span id="LC3326" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">eff</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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3327
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<pre style="margin: 0;"> <span id="LC3327" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dontcalcimportance_half( njob, eff, bseq, localhomtable ); // CHUUI</span></span>
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<pre style="margin: 0;"> <span id="LC3328" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3329" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#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">@@ -1406,9 +1406,9 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],</td>
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="c"> <span class="n" style="color: #333;">counteff_simple</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span> <span class="p">);</span></span>
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1408
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">ntarget</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">locnjob</span> <span class="p">)</span></span>
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1409
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1412
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> <span class="p">}</span></span>
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1413
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1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"></span>
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">weight</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1631,9 +1631,9 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],</td>
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1631
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1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="c"> <span class="p">{</span></span>
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1632
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1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="c"> <span class="n" style="color: #333;">counteff_simple</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span> <span class="p">);</span></span>
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1633
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1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">ntarget</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">locnjob</span> <span class="p">)</span></span>
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1634
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<td class="new_line diff-line-num old" data-linenumber="1634" 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="LC1634" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span> <span class="p">);</span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_target</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">ntarget</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">targetmap</span><span class="p">,</span> <span class="n" style="color: #333;">targetmapr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1636
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<pre style="margin: 0;">-<span id="LC1636" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span> <span class="p">);</span></span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="c"> <span class="n" style="color: #333;">calcimportance_half</span><span class="p">(</span> <span class="n" style="color: #333;">locnjob</span><span class="p">,</span> <span class="n" style="color: #333;">effarrforlocalhom</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alloclen</span></span> <span class="p">);</span></span>
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1637
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c"> <span class="p">}</span></span>
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1638
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="c"> <span class="p">}</span></span>
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1639
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1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="c"> </span>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">progs="_PROGS"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">progs="$progs dash_client"</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">for prog in $progs; do</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> printf $prog" "</span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">done</span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">make clean</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">make CC="$HOME/soft/gcc/usr/local/bin/gcc" CFLAGS="-O3 -m32 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5 -static-libgcc" LIBS="-lm -lpthread -lgcc_eh" ENABLE_MULTITHREAD="-Denablemultithread"</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">make CC="clang" CFLAGS="-O3 -arch x86_64 -mmacosx-version-min=10.9 -DMACOSX_DEPLOYMENT_TARGET=10.9" LIBS="-lm -lpthread" ENABLE_MULTITHREAD="-Denablemultithread"</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">env CC='clang -O3 -arch x86_64' GOARCH=amd64 GOOS=darwin CGO_ENABLED=0 go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki</span>
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8
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">for prog in $progs; do</span>
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9
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> mv $prog $prog.<span class="idiff left right">intel32</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> mv $prog $prog.<span class="idiff left right">x86_64</span></span>
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10
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">done</span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">make clean</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">make CC="$HOME/soft/gcc/usr/local/bin/gcc" CFLAGS="-O3 -m64 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5 -static-libgcc" LIBS="-lm -lpthread -lgcc_eh" ENABLE_MULTITHREAD="-Denablemultithread"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">make CC="clang" CFLAGS="-O3 -arch arm64 -mmacosx-version-min=11.1 -DMACOSX_DEPLOYMENT_TARGET=11.1" LIBS="-lm -lpthread" ENABLE_MULTITHREAD="-Denablemultithread"</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">env CC='clang -O3 -arch arm64' GOARCH=arm64 GOOS=darwin CGO_ENABLED=0 go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki</span>
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14
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">for prog in $progs; do</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> mv $prog $prog.<span class="idiff left right">intel</span>64</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> mv $prog $prog.<span class="idiff left right">arm</span>64</span>
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16
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">done</span>
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17
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="18" 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">
18
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<td class="new_line diff-line-num old" data-linenumber="21" 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="LC18" class="line" lang="plaintext">#make clean</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">#make CC="gcc-4.0" CFLAGS="-arch ppc64 -m64 -O3 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5" ENABLE_MULTITHREAD=""</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">#for prog in $progs; do</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"># mv $prog $prog.ppc64</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">#done</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#</span>
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<td class="old_line diff-line-num old" data-linenumber="24" 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">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#make clean</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#make CC="gcc-4.0" CFLAGS="-arch ppc -m32 -O3 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5" ENABLE_MULTITHREAD=""</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">#for prog in $progs; do</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"># mv $prog $prog.ppc32</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">#done</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">set $progs</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">for prog in $progs; do</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># lipo -create $prog.icc $prog.ppc32 $prog.ppc64 -output $prog</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># lipo -create $prog.intel64 $prog.intel32 $prog.ppc32 $prog.ppc64 -output $prog</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> lipo -create $prog.<span class="idiff left">intel</span>64 $prog.<span class="idiff right">intel32</span> -output $prog</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> lipo -create $prog.<span class="idiff left">x86_</span>64 $prog.<span class="idiff right">arm64</span> -output $prog</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> cp $prog ../binaries</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">done</span></pre>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/82da29e9f1abd9a8a5798273dad78db14009d9da#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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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.4<span class="idiff left">75</span>, 202<span class="idiff">0/Nov</span>/2<span class="idiff right">3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.4<span class="idiff left">81</span>, 202<span class="idiff">1/May</span>/2<span class="idiff right">6</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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6
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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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