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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/084720ae6bcfcbd90efef804bf7aa7bb16731de4">084720ae</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-24T02:02:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.486</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#b384af181f78447eab2d9f5cdac9be6d48ed8526">
MPI/pairlocalalign_mpi.c
</a>
</li>
<li class="file-stats">
<a href="#fd2fcf5d0ea2e2b107645a0d51990eea552f2b2e">
core/MSalignmm.c
</a>
</li>
<li class="file-stats">
<a href="#c08901e9ce7c420c65030b96053a390841b4a8cc">
core/Salignmm.c
</a>
</li>
<li class="file-stats">
<a href="#a0ceacde4b98f9b54a66b69e1010719564b2ba72">
core/disttbfast.c
</a>
</li>
<li class="file-stats">
<a href="#58e2e0082bb4ca16bc55a2289e58d89f679360a0">
core/functions.h
</a>
</li>
<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>
<li class="file-stats">
<a href="#091f6a935329e8080a6bea490141fb6a5b924660">
core/mtxutl.c
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<li class="file-stats">
<a href="#93f296c20fdcfe44e5dd58f323ceeddf6c24e552">
core/pairlocalalign.c
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</li>
<li class="file-stats">
<a href="#6f036ff28d08d3462cd8f0b59de73fb1b1636ed2">
core/pairlocalalignmain.c
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<li class="file-stats">
<a href="#b3a870840642b1943f3cb55ad3a88066fdb6d139">
<span class="deleted-file">
−
core/serial.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="#5584b7e2129a1bb4aa5dabe72bb6a85d2efa2d9f">
core/univscript.tmpl
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<li class="file-stats">
<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
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<h4>Changes:</h4>
<li id="b384af181f78447eab2d9f5cdac9be6d48ed8526">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#b384af181f78447eab2d9f5cdac9be6d48ed8526"><strong>MPI/pairlocalalign_mpi.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="72" 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">@@ -72,6 +72,7 @@ typedef struct _thread_arg</td>
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<td class="old_line diff-line-num" data-linenumber="72" 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">
72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" 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;">targetmap</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC75" 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;">expdist</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
75
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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mutex_counter</span><span class="p">;</span></span>
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76
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<td class="new_line diff-line-num" data-linenumber="77" 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">
77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mutex_stdout</span><span class="p">;</span></span>
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77
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<td class="new_line diff-line-num" data-linenumber="78" 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">
78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">thread_arg_t</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1973" 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="1974" 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">@@ -1973,6 +1974,7 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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1973
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1974
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1974" class="line" lang="c"> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lastresx</span><span class="p">;</span></span>
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1974
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1975
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1975" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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1975
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1976
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<pre style="margin: 0;"> <span id="LC1976" 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;">targetmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">targetmap</span><span class="p">;</span></span>
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1977
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<pre style="margin: 0;">+<span id="LC1977" 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;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">expdist</span><span class="p">;</span></span>
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1976
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<td class="new_line diff-line-num" data-linenumber="1978" 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">
1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="c"></span>
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1977
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "thread %d start!\n", thread_no );</span></span>
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1978
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1980
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<pre style="margin: 0;"> <span id="LC1980" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2138" 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="2140" 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">@@ -2138,7 +2140,10 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2138
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<td class="new_line diff-line-num" data-linenumber="2140" 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">
2140
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<pre style="margin: 0;"> <span id="LC2140" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2139
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<td class="new_line diff-line-num" data-linenumber="2141" 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">
2141
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<pre style="margin: 0;"> <span id="LC2141" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2140
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2142
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<pre style="margin: 0;"> <span id="LC2142" class="line" lang="c"> <span class="p">{</span></span>
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2141
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<pre style="margin: 0;">-<span id="LC2141" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2146
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<pre style="margin: 0;">+<span id="LC2146" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2142
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">scoreoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</span> <span class="p">)</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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2143
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="c"> <span class="p">{</span></span>
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2144
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2149
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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2193" 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="2198" 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">@@ -2193,8 +2198,11 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2193
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2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2194
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2199
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<pre style="margin: 0;"> <span id="LC2199" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2195
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2200
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<pre style="margin: 0;"> <span id="LC2200" class="line" lang="c"> <span class="p">{</span></span>
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2196
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<pre style="margin: 0;">-<span id="LC2196" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2197
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<pre style="margin: 0;">-<span id="LC2197" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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2198
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2206
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2199
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2207
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<pre style="margin: 0;"> <span id="LC2207" class="line" lang="c"> <span class="p">{</span></span>
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2200
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2208
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<pre style="margin: 0;"> <span id="LC2208" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2231" 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="2239" 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">@@ -2231,7 +2239,10 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2231
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2239
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<pre style="margin: 0;"> <span id="LC2239" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2232
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<td class="new_line diff-line-num" data-linenumber="2240" 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">
2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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<td class="old_line diff-line-num" data-linenumber="2233" 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">
2233
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<td class="new_line diff-line-num" data-linenumber="2241" 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">
2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="c"> <span class="p">{</span></span>
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2234
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<td class="new_line diff-line-num old" data-linenumber="2242" 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="LC2234" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2235
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2236
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="c"> <span class="p">{</span></span>
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2237
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2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2374" 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="2385" 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">@@ -2374,7 +2385,7 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2374
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2385
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="c"><span class="p">}</span></span>
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2375
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2386
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2376
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2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="c"></span>
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2377
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<pre style="margin: 0;">-<span id="LC2377" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairalign</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;">name</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;">nlen</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">aseq</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;">dseq</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;">thereisxineachseq</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;">mseq1</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;">mseq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span> <span class="p">)</span></span>
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2388
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairalign</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;">name</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;">nlen</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">aseq</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;">dseq</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;">thereisxineachseq</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;">mseq1</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;">mseq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</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">expdist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span> <span class="p">)</span></span>
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2378
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2389
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<pre style="margin: 0;"> <span id="LC2389" class="line" lang="c"><span class="p">{</span></span>
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2379
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2390
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<pre style="margin: 0;"> <span id="LC2390" 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;">ilim</span><span class="p">,</span> <span class="n" style="color: #333;">jst</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="p">;</span></span>
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2380
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2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">off1</span><span class="p">,</span> <span class="n" style="color: #333;">off2</span><span class="p">,</span> <span class="n" style="color: #333;">dum1</span><span class="p">,</span> <span class="n" style="color: #333;">dum2</span><span class="p">,</span> <span class="n" style="color: #333;">thereisx</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2616" 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="2627" 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">@@ -2616,6 +2627,7 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2616
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2627
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<pre style="margin: 0;"> <span id="LC2627" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bpp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpp</span><span class="p">;</span> </span>
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<td class="old_line diff-line-num" data-linenumber="2617" 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">
2617
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<td class="new_line diff-line-num" data-linenumber="2628" 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">
2628
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<pre style="margin: 0;"> <span id="LC2628" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">lastresx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastresx</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2618" 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">
2618
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2629
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<pre style="margin: 0;"> <span id="LC2629" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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2630
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<pre style="margin: 0;">+<span id="LC2630" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">;</span></span>
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2619
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2631
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<pre style="margin: 0;"> <span id="LC2631" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">targetmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targetmap</span><span class="p">;</span></span>
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2620
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2632
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<pre style="margin: 0;"> <span id="LC2632" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mutex_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_counter</span><span class="p">;</span></span>
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2621
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2633
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<pre style="margin: 0;"> <span id="LC2633" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mutex_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_stdout</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2724" 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="2736" 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">@@ -2724,8 +2736,11 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2724
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2736
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<pre style="margin: 0;"> <span id="LC2736" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2725
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2737
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<pre style="margin: 0;"> <span id="LC2737" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2726
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2738
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<pre style="margin: 0;"> <span id="LC2738" class="line" lang="c"> <span class="p">{</span></span>
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2727
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<pre style="margin: 0;">-<span id="LC2727" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2728
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<td class="new_line diff-line-num old" data-linenumber="2739" 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="LC2728" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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2739
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<pre style="margin: 0;">+<span id="LC2739" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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2740
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<pre style="margin: 0;">+<span id="LC2740" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2741
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<pre style="margin: 0;">+<span id="LC2741" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2742
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<pre style="margin: 0;">+<span id="LC2742" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2743
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<pre style="margin: 0;">+<span id="LC2743" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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2729
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2744
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<pre style="margin: 0;"> <span id="LC2744" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2730
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2745
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<pre style="margin: 0;"> <span id="LC2745" class="line" lang="c"> <span class="p">{</span></span>
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2731
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2746
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<pre style="margin: 0;"> <span id="LC2746" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2762" 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="2777" 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">@@ -2762,7 +2777,10 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2762
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2777
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<pre style="margin: 0;"> <span id="LC2777" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2763
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2778
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<pre style="margin: 0;"> <span id="LC2778" class="line" lang="c"> <span class="p">{</span></span>
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2764
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<td class="new_line diff-line-num" data-linenumber="2779" 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">
2779
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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "dist = %f\n", score2dist( pscore, selfscore[i], selfscore[j] ) );</span></span>
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2765
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<pre style="margin: 0;">-<span id="LC2765" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2780
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<pre style="margin: 0;">+<span id="LC2780" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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2781
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<pre style="margin: 0;">+<span id="LC2781" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2782
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<pre style="margin: 0;">+<span id="LC2782" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2783
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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2766
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2784
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<pre style="margin: 0;"> <span id="LC2784" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2767
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2785
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<pre style="margin: 0;"> <span id="LC2785" class="line" lang="c"> <span class="p">{</span></span>
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2768
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2786
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<pre style="margin: 0;"> <span id="LC2786" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2806" 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="2824" 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">@@ -2806,7 +2824,10 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2806
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2824
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<pre style="margin: 0;"> <span id="LC2824" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2807
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<td class="new_line diff-line-num" data-linenumber="2825" 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">
2825
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<pre style="margin: 0;"> <span id="LC2825" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2808
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<td class="new_line diff-line-num" data-linenumber="2826" 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">
2826
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<pre style="margin: 0;"> <span id="LC2826" class="line" lang="c"> <span class="p">{</span></span>
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2809
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<td class="new_line diff-line-num old" data-linenumber="2827" 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="LC2809" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2827
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<pre style="margin: 0;">+<span id="LC2827" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2828
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<pre style="margin: 0;">+<span id="LC2828" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2829
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<pre style="margin: 0;">+<span id="LC2829" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2830
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<pre style="margin: 0;">+<span id="LC2830" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2810
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<td class="new_line diff-line-num" data-linenumber="2831" 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">
2831
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<pre style="margin: 0;"> <span id="LC2831" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">scoreoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</span> <span class="p">)</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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2811
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2832
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<pre style="margin: 0;"> <span id="LC2832" class="line" lang="c"> <span class="p">{</span></span>
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2812
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2833
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<pre style="margin: 0;"> <span id="LC2833" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3059" 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="3080" 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">@@ -3059,7 +3080,7 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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3059
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3080
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<pre style="margin: 0;"> <span id="LC3080" class="line" lang="c"><span class="p">}</span></span>
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3060
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3081
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<pre style="margin: 0;"> <span id="LC3081" class="line" lang="c"></span>
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3061
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3082
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<pre style="margin: 0;"> <span id="LC3082" class="line" lang="c"></span>
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3062
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<pre style="margin: 0;">-<span id="LC3062" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</span> <span class="p">)</span></span>
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3083
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<pre style="margin: 0;">+<span id="LC3083" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</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">double</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">expdist</span></span> <span class="p">)</span></span>
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3084
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<pre style="margin: 0;"> <span id="LC3084" class="line" lang="c"><span class="p">{</span></span>
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3085
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<pre style="margin: 0;"> <span id="LC3085" 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;">nlen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thereisxineachseq</span><span class="p">;</span></span>
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3086
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<pre style="margin: 0;"> <span id="LC3086" class="line" lang="c"> <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;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3214" 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="3235" 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">@@ -3214,7 +3235,7 @@ int pairlocalalign( int ngui, int lgui, char **namegui, char **seqgui, double **</td>
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3214
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3235
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<pre style="margin: 0;"> <span id="LC3235" class="line" lang="c"> <span class="n" style="color: #333;">thereisxineachseq</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;">removex</span><span class="p">(</span> <span class="n" style="color: #333;">dseq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">bseq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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3215
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3236
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<pre style="margin: 0;"> <span id="LC3236" class="line" lang="c"> <span class="p">}</span></span>
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3237
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<pre style="margin: 0;"> <span id="LC3237" class="line" lang="c"></span>
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3217
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<pre style="margin: 0;">-<span id="LC3217" class="line" lang="c"> <span class="n" style="color: #333;">pairalign</span><span class="p">(</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">dseq</span><span class="p">,</span> <span class="n" style="color: #333;">thereisxineachseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">lastresx</span><span class="p">,</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">ngui</span> <span class="p">);</span></span>
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3238
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<pre style="margin: 0;">+<span id="LC3238" class="line" lang="c"> <span class="n" style="color: #333;">pairalign</span><span class="p">(</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">dseq</span><span class="p">,</span> <span class="n" style="color: #333;">thereisxineachseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">lastresx</span><span class="p">,</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">expdist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ngui</span> <span class="p">);</span></span>
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3218
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3239
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<pre style="margin: 0;"> <span id="LC3239" class="line" lang="c"></span>
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3219
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3240
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<pre style="margin: 0;"> <span id="LC3240" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span><span class="p">,</span> <span class="s" style="color: #d14;">"done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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3220
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3241
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<pre style="margin: 0;"> <span id="LC3241" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if DEBUG</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#fd2fcf5d0ea2e2b107645a0d51990eea552f2b2e"><strong>core/MSalignmm.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">@@ -2091,9 +2091,10 @@ static void freearrays(</td>
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2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mgt2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalignmm</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;">n_dynamicmtx</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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;">sgap1</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;">sgap2</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;">egap1</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;">egap2</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;">chudanpt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chudanref</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;">chudanres</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</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;">cpmxchild0</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;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalignmm</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;">n_dynamicmtx</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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;">sgap1</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;">sgap2</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;">egap1</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;">egap2</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;">chudanpt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chudanref</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;">chudanres</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */</span></span>
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2098" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// int k;</span></span>
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<pre style="margin: 0;"> <span id="LC2099" 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>
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ll1</span><span class="p">,</span> <span class="n" style="color: #333;">ll2</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">@@ -2192,14 +2193,14 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,</td>
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<pre style="margin: 0;"> <span id="LC2193" class="line" lang="c"> <span class="p">}</span></span>
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2194
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<pre style="margin: 0;"> <span id="LC2194" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2195" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC2195" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2196" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><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">cpmxchild0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nUse cpmxhist for child 0!\n" );</span></span>
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<pre style="margin: 0;">-<span id="LC2198" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2200" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if ATO</span></span>
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<pre style="margin: 0;">-<span id="LC2200" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC2201" class="line" lang="c"> <span class="n" style="color: #333;">ogcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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2202
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<pre style="margin: 0;">-<span id="LC2202" class="line" lang="c"> <span class="n" style="color: #333;">fgcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="c"> <span class="n" style="color: #333;">ogcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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="LC2203" class="line" lang="c"> <span class="n" style="color: #333;">fgcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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<pre style="margin: 0;"> <span id="LC2204" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2205
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<pre style="margin: 0;"> <span id="LC2205" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2219" 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">@@ -2219,14 +2220,14 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,</td>
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<pre style="margin: 0;"> <span id="LC2220" 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="LC2221" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2222" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC2222" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2223" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><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">cpmxchild1</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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2223
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<pre style="margin: 0;"> <span id="LC2224" class="line" lang="c"> <span class="p">{</span></span>
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2224
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2225
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<pre style="margin: 0;"> <span id="LC2225" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nUse cpmxhist for child 1!\n" );</span></span>
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<pre style="margin: 0;">-<span id="LC2225" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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2226
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2227" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if ATO</span></span>
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<pre style="margin: 0;">-<span id="LC2227" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC2228" class="line" lang="c"> <span class="n" style="color: #333;">ogcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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="LC2229" class="line" lang="c"> <span class="n" style="color: #333;">fgcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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<pre style="margin: 0;">+<span id="LC2228" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC2229" class="line" lang="c"> <span class="n" style="color: #333;">ogcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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="LC2230" class="line" lang="c"> <span class="n" style="color: #333;">fgcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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<pre style="margin: 0;"> <span id="LC2231" 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="LC2232" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</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">@@ -2478,15 +2479,17 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,</td>
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<pre style="margin: 0;"> <span id="LC2479" 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="LC2480" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2481" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// matomete free</span></span>
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<pre style="margin: 0;">-<span id="LC2481" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cpmx1</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC2482" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cpmx1</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cpmxchild0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff right"> </span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC2483" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2484" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxchild0\n" );</span></span>
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<pre style="margin: 0;">-<span id="LC2484" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxchild0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2487" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cpmx2</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC2488" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cpmx2</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cpmxchild1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff right"> </span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC2489" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2490" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxchild1\n" );</span></span>
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<pre style="margin: 0;">-<span id="LC2489" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2491" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxchild1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2492" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2493" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2494" 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">@@ -605,7 +605,7 @@ static void Atracking_localhom( double *impwmpt, double *lasthorizontalw, double</td>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">createcpmxresult</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</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="n" style="color: #333;">eff2</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;">cpmx1</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;">cpmx2</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;">gaptable1</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;">gaptable2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">usehist1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// allocate, free ryouhou suru.</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">createcpmxresult</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</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="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmx2</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;">gaptable1</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;">gaptable2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">usehist1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// allocate, free ryouhou suru.</span></span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC610" 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;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">gaptable1</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">@@ -623,7 +623,7 @@ static void createcpmxresult( double **cpmxresult, int limk, double eff1, double</td>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="c"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if( amino_n['-'] == i ) cpmxresult[amino_n['-']][j] = eff1; // tsukawanai</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="c"> <span class="n" style="color: #333;">cpmxresult</span><span class="p">[</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cpmx1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eff1</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;">cpmxresult</span><span class="p">[</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="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmx1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eff1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC629" 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;">p</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;">alen</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -632,16 +632,32 @@ static void createcpmxresult( double **cpmxresult, int limk, double eff1, double</td>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if( amino_n['-'] == i ) cpmxresult[amino_n['-']][j] = eff2; // tsukawanai</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">cpmxresult</span><span class="p">[</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cpmx2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eff2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">cpmxresult</span><span class="p">[</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="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmx2</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eff2</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>
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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;">usehist1</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// cpmx1[i] = NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// cpmx2[i] = NULL;</span></span>
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638
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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;">usehist1</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="p">{</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx1</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="c"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx1</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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="c"> <span class="p">}</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</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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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx2</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="c"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx2</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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="c"> <span class="p">}</span></span>
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648
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<pre style="margin: 0;"> <span id="LC648" 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;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist1</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span> <span class="p">);</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist1</span> <span class="p">)</span> </span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="c"> <span class="p">{</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx1</span> <span class="p">);</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="c"> <span class="p">}</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">usehist2</span> <span class="p">)</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmx2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC660" 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="LC661" 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="LC662" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC663" 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">@@ -1067,7 +1083,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw,</td>
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="n" style="color: #333;">wm</span> <span class="p">);</span></span>
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="c"><span class="p">}</span></span>
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align</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;">n_dynamicmtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_l</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_ex_l</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">sgap1</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;">sgap2</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;">egap1</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;">egap2</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;">chudanpt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chudanref</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;">chudanres</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstmem</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">calledbyfulltreebase</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;">cpmxchild0</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;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align</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;">n_dynamicmtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_l</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_ex_l</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">sgap1</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;">sgap2</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;">egap1</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;">egap2</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;">chudanpt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chudanref</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;">chudanres</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstmem</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">calledbyfulltreebase</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">)</span></span>
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */</span></span>
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="c"><span class="p">{</span></span>
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1073
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1128" 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">@@ -1112,9 +1128,9 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1112
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</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;">fgcp2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fgcp2o</span><span class="p">;</span></span>
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1113
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1129
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<pre style="margin: 0;"> <span id="LC1129" 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;">ogcp1opt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ogcp2opt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fgcp1opt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fgcp2opt</span><span class="p">;</span></span>
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1114
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<td class="new_line diff-line-num" data-linenumber="1130" 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">
1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</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;">cpmx1</span><span class="p">;</span></span>
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1115
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<td class="new_line diff-line-num old" data-linenumber="1131" 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="LC1115" 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;">cpmx1pt</span><span class="p">;</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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1116
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</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;">cpmx2</span><span class="p">;</span></span>
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1117
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<td class="new_line diff-line-num old" data-linenumber="1133" 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="LC1117" 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;">cpmx2pt</span><span class="p">;</span></span>
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1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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1118
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</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;">intwork</span><span class="p">;</span></span>
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1119
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</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;">doublework</span><span class="p">;</span></span>
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1120
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TLS</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orlgth1</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;">orlgth2</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1461" 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="1477" 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">@@ -1461,19 +1477,19 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1461
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1477
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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="c"> <span class="p">}</span></span>
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1462
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<td class="new_line diff-line-num" data-linenumber="1478" 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">
1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="c"></span>
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1463
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1479
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="c"></span>
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1464
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<pre style="margin: 0;">-<span id="LC1464" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span></span>
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1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><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">cpmxchild0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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1465
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1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="c"> <span class="p">{</span></span>
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1466
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1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nUse cpmxhist for child 0!\n" );</span></span>
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1467
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<pre style="margin: 0;">-<span id="LC1467" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">;</span></span>
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1468
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<pre style="margin: 0;">-<span id="LC1468" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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1469
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<pre style="margin: 0;">-<span id="LC1469" class="line" lang="c"> <span class="n" style="color: #333;">ogcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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1470
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<pre style="margin: 0;">-<span id="LC1470" class="line" lang="c"> <span class="n" style="color: #333;">fgcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>;</span></span>
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1484
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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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1485
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="c"> <span class="n" style="color: #333;">ogcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="c"> <span class="n" style="color: #333;">fgcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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1471
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1487
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<pre style="margin: 0;"> <span id="LC1487" class="line" lang="c"> <span class="p">}</span></span>
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1472
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1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1473
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1489
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="c"> <span class="p">{</span></span>
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1474
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1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nDo not use cpmxhist for child 0!\n" );</span></span>
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1475
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<pre style="margin: 0;">-<span id="LC1475" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmx1</span><span class="p">;</span></span>
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1476
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<pre style="margin: 0;">-<span id="LC1476" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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1491
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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">cpmx1</span><span class="p">;</span></span>
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1492
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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1477
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1493
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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="c"></span>
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1478
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1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfreq1</span><span class="p">;</span></span>
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1479
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1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="c"> <span class="n" style="color: #333;">gapcountf</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq1pt</span><span class="p">,</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1485" 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="1501" 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">@@ -1485,19 +1501,19 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1485
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1501
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<pre style="margin: 0;"> <span id="LC1501" class="line" lang="c"> <span class="n" style="color: #333;">st_FinalGapCount</span><span class="p">(</span> <span class="n" style="color: #333;">fgcp1opt</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span> <span class="p">);</span></span>
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1486
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1502
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<pre style="margin: 0;"> <span id="LC1502" class="line" lang="c"> <span class="p">}</span></span>
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1487
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1503
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<pre style="margin: 0;"> <span id="LC1503" class="line" lang="c"> </span>
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1488
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<pre style="margin: 0;">-<span id="LC1488" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="p">)</span></span>
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1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><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">cpmxchild1</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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1489
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1505
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<pre style="margin: 0;"> <span id="LC1505" class="line" lang="c"> <span class="p">{</span></span>
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1490
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<td class="new_line diff-line-num" data-linenumber="1506" 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">
1506
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<pre style="margin: 0;"> <span id="LC1506" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nUse cpmxhist for child 1!\n" );</span></span>
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1491
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<pre style="margin: 0;">-<span id="LC1491" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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1492
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<pre style="margin: 0;">-<span id="LC1492" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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1493
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<pre style="margin: 0;">-<span id="LC1493" class="line" lang="c"> <span class="n" style="color: #333;">ogcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1494" 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">
1494
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<td class="new_line diff-line-num old" data-linenumber="1507" 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="LC1494" class="line" lang="c"> <span class="n" style="color: #333;">fgcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">[</span><span class="n" style="color: #333;">nalphabets</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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1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>;</span></span>
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1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</span><span class="p">];</span></span>
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1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="c"> <span class="n" style="color: #333;">ogcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="c"> <span class="n" style="color: #333;">fgcp2opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;">cpmxchild1</span><span class="p"><span class="idiff right">)</span>[</span><span class="n" style="color: #333;">nalphabets</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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1495
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<td class="new_line diff-line-num" data-linenumber="1511" 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">
1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="c"> <span class="p">}</span></span>
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1496
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<td class="new_line diff-line-num" data-linenumber="1512" 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">
1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1497
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<td class="new_line diff-line-num" data-linenumber="1513" 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">
1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="c"> <span class="p">{</span></span>
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1498
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<td class="new_line diff-line-num" data-linenumber="1514" 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">
1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nDo not use cpmxhist for child 1!\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1499" 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">
1499
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<td class="new_line diff-line-num old" data-linenumber="1515" 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="LC1499" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmx2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1500" 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">
1500
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<pre style="margin: 0;">-<span id="LC1500" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">jcyc</span> <span class="p">);</span></span>
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1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">cpmx2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">jcyc</span> <span class="p">);</span></span>
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1501
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1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="c"></span>
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1502
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1518
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<pre style="margin: 0;"> <span id="LC1518" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfreq2</span><span class="p">;</span></span>
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1503
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1519
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<pre style="margin: 0;"> <span id="LC1519" class="line" lang="c"> <span class="n" style="color: #333;">gapcountf</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq2pt</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1534" 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">@@ -1518,8 +1534,8 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1518
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="c"> <span class="p">}</span></span>
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1519
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1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1520
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1536
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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="c"> <span class="p">{</span></span>
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1521
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<td class="new_line diff-line-num old" data-linenumber="1537" 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="LC1521" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmx1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1522" 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">
1522
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<td class="new_line diff-line-num old" data-linenumber="1537" 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="LC1522" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmx2</span><span class="p">;</span></span>
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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="c"> <span class="n" style="color: #333;">cpmx1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">cpmx1</span><span class="p">;</span></span>
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1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="c"> <span class="n" style="color: #333;">cpmx2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">cpmx2</span><span class="p">;</span></span>
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1523
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1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfreq1</span><span class="p">;</span></span>
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1524
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1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="c"> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfreq2</span><span class="p">;</span></span>
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1525
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="c"> <span class="n" style="color: #333;">ogcp1opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ogcp1o</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1530" 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="1546" 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">@@ -1530,14 +1546,14 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1530
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1546
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">reuseprofiles</span> <span class="p">)</span></span>
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1531
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="c"> <span class="p">{</span></span>
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1532
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1548
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "reuse" );</span></span>
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1533
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<pre style="margin: 0;">-<span id="LC1533" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_add</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_add</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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1534
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1550
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<pre style="margin: 0;"> <span id="LC1550" class="line" lang="c"> <span class="p">}</span></span>
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1535
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1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="1536" 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">
1536
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<td class="new_line diff-line-num" data-linenumber="1552" 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">
1552
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1537" 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">
1537
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<td class="new_line diff-line-num" data-linenumber="1553" 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">
1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "new profile" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1538" 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">
1538
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<td class="new_line diff-line-num old" data-linenumber="1554" 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="LC1538" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff1</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">icyc</span> <span class="p">);</span></span>
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1539
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<td class="new_line diff-line-num" data-linenumber="1555" 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">
1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1540" 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">
1540
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<td class="new_line diff-line-num old" data-linenumber="1556" 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="LC1540" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">jcyc</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1556
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="c"> <span class="n" style="color: #333;">cpmx_calc_new</span><span class="p">(</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">eff2</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">jcyc</span> <span class="p">);</span></span>
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1541
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<td class="new_line diff-line-num" data-linenumber="1557" 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">
1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1542" 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">
1542
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<td class="new_line diff-line-num" data-linenumber="1558" 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">
1558
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<pre style="margin: 0;"> <span id="LC1558" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">sgap1</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1543" 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">
1543
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<td class="new_line diff-line-num" data-linenumber="1559" 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">
1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1614" 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="1630" 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">@@ -1614,7 +1630,7 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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<td class="old_line diff-line-num" data-linenumber="1614" 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">
1614
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<td class="new_line diff-line-num" data-linenumber="1630" 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">
1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1615" 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">
1615
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<td class="new_line diff-line-num" data-linenumber="1631" 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">
1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%3d ", i );</span></span>
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<td class="old_line diff-line-num" data-linenumber="1616" 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">
1616
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<td class="new_line diff-line-num" data-linenumber="1632" 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">
1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; j<nalphabets; j++ ) </span></span>
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<td class="old_line diff-line-num old" data-linenumber="1617" 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">
1617
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<td class="new_line diff-line-num old" data-linenumber="1633" 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="LC1617" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%4.2f ", cpmx1pt[j][i] );</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%4.2f ", <span class="idiff left">(*</span>cpmx1pt<span class="idiff right">)</span>[j][i] );</span></span>
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<td class="old_line diff-line-num" data-linenumber="1618" 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">
1618
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<td class="new_line diff-line-num" data-linenumber="1634" 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">
1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num" data-linenumber="1619" 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">
1619
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<td class="new_line diff-line-num" data-linenumber="1635" 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">
1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="1620" 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">
1620
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<td class="new_line diff-line-num" data-linenumber="1636" 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">
1636
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<pre style="margin: 0;"> <span id="LC1636" 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 old_line" data-linenumber="1628" 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="1644" 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">@@ -1628,7 +1644,7 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1628
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<td class="new_line diff-line-num" data-linenumber="1644" 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">
1644
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num" data-linenumber="1629" 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">
1629
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<td class="new_line diff-line-num" data-linenumber="1645" 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">
1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%3d ", i );</span></span>
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1630
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; j<nalphabets; j++ ) </span></span>
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1631
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<pre style="margin: 0;">-<span id="LC1631" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%4.2f ", cpmx2pt[j][i] );</span></span>
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1647
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "%4.2f ", <span class="idiff left">(*</span>cpmx2pt<span class="idiff right">)</span>[j][i] );</span></span>
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1632
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1648
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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1633
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1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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1634
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\ngapfreq1 = " );</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1681" 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="1697" 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">@@ -1681,11 +1697,11 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **</td>
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1681
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="c"> <span class="n" style="color: #333;">currentw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w1</span><span class="p">;</span></span>
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1682
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1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="c"> <span class="n" style="color: #333;">previousw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w2</span><span class="p">;</span></span>
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1683
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1699
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<pre style="margin: 0;"> <span id="LC1699" class="line" lang="c"></span>
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1684
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<pre style="margin: 0;">-<span id="LC1684" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">initverticalw</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">initverticalw</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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1685
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1701
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<pre style="margin: 0;"> <span id="LC1701" 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="p">)</span></span>
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1686
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<td class="new_line diff-line-num" data-linenumber="1702" 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">
1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="c"> <span class="n" style="color: #333;">imp_match_out_vead_tate</span><span class="p">(</span> <span class="n" style="color: #333;">initverticalw</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth1</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 060306</span></span>
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1687
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1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="c"></span>
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1688
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<td class="new_line diff-line-num old" data-linenumber="1704" 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="LC1688" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">currentw</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">currentw</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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1689
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1705
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<pre style="margin: 0;"> <span id="LC1705" 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="p">)</span></span>
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1690
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<td class="new_line diff-line-num" data-linenumber="1706" 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">
1706
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="c"> <span class="n" style="color: #333;">imp_match_out_vead</span><span class="p">(</span> <span class="n" style="color: #333;">currentw</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 060306</span></span>
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1691
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 // -> tbfast.c // impossible</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1826" 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">@@ -1810,7 +1826,7 @@ for( i=0; i<lgth2; i++ )</td>
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1810
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1826
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<pre style="margin: 0;"> <span id="LC1826" class="line" lang="c"></span>
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1811
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1827
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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="c"> <span class="n" style="color: #333;">previousw</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initverticalw</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;">1</span><span class="p">];</span></span>
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1812
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1828
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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="1813" 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">
1813
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<td class="new_line diff-line-num old" data-linenumber="1829" 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="LC1813" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">currentw</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1829
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<pre style="margin: 0;">+<span id="LC1829" class="line" lang="c"> <span class="n" style="color: #333;">match_calc</span><span class="p">(</span> <span class="n" style="color: #333;">n_dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">currentw</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">lgth2</span><span class="p">,</span> <span class="n" style="color: #333;">doublework</span><span class="p">,</span> <span class="n" style="color: #333;">intwork</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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1814
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1830
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if XXXXXXX</span></span>
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1815
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1831
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<pre style="margin: 0;"> <span id="LC1831" 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;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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1816
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1832
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<pre style="margin: 0;"> <span id="LC1832" 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;">"i=%d</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;">i</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2092" 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="2108" 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">@@ -2092,18 +2108,18 @@ fprintf( stderr, "\n" );</td>
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2092
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2108
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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2093
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2109
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<pre style="margin: 0;"> <span id="LC2109" class="line" lang="c"> </span>
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2094
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<td class="new_line diff-line-num" data-linenumber="2110" 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">
2110
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<pre style="margin: 0;"> <span id="LC2110" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">nalphabets</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// gapcount, opg, fng no bun</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2095" 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">
2095
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<td class="new_line diff-line-num old" data-linenumber="2111" 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="LC2095" class="line" lang="c"> <span class="n" style="color: #333;">createcpmxresult</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span><span class="p">,</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff1</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff2</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">gt1</span><span class="p">,</span> <span class="n" style="color: #333;">gt2</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">)</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// naka de free</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="c"> <span class="n" style="color: #333;">createcpmxresult</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span><span class="p">,</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff1</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff2</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx1pt</span><span class="p">,</span> <span class="n" style="color: #333;">cpmx2pt</span><span class="p">,</span> <span class="n" style="color: #333;">gt1</span><span class="p">,</span> <span class="n" style="color: #333;">gt2</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmx1pt</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=<span class="idiff right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span><span class="p">)</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// naka de free</span></span>
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2096
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<td class="new_line diff-line-num" data-linenumber="2112" 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">
2112
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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="c"> <span class="n" style="color: #333;">creategapfreqresult</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nalphabets</span><span class="p">,</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff1</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff2</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq1pt</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq2pt</span><span class="p">,</span> <span class="n" style="color: #333;">gt1</span><span class="p">,</span> <span class="n" style="color: #333;">gt2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// naka deha free shinai</span></span>
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2097
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<td class="new_line diff-line-num" data-linenumber="2113" 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">
2113
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<pre style="margin: 0;"> <span id="LC2113" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// gapfreq1, gapfreq2 ha mada tsukau</span></span>
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2098
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2114
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<pre style="margin: 0;"> <span id="LC2114" class="line" lang="c"> <span class="n" style="color: #333;">createogresult</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nalphabets</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff1</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff2</span><span class="p">,</span> <span class="n" style="color: #333;">ogcp1opt</span><span class="p">,</span> <span class="n" style="color: #333;">ogcp2opt</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq1pt</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq2pt</span><span class="p">,</span> <span class="n" style="color: #333;">gt1</span><span class="p">,</span> <span class="n" style="color: #333;">gt2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// naka deha free shinai</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2099" 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">
2099
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<td class="new_line diff-line-num old" data-linenumber="2115" 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="LC2099" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ogcp1opt</span> <span class="p">);</span></span>
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2100
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<td class="new_line diff-line-num old" data-linenumber="2115" 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="LC2100" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ogcp2opt</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ogcp1opt</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">ogcp2opt</span> <span class="p">);</span></span>
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2101
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<td class="new_line diff-line-num" data-linenumber="2117" 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">
2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="c"> <span class="n" style="color: #333;">createfgresult</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpmxresult</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nalphabets</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">limk</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff1</span><span class="p">,</span> <span class="n" style="color: #333;">totaleff2</span><span class="p">,</span> <span class="n" style="color: #333;">fgcp1opt</span><span class="p">,</span> <span class="n" style="color: #333;">fgcp2opt</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq1pt</span><span class="p">,</span> <span class="n" style="color: #333;">gapfreq2pt</span><span class="p">,</span> <span class="n" style="color: #333;">gt1</span><span class="p">,</span> <span class="n" style="color: #333;">gt2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// naka deha free shinai</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2102" 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">
2102
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<td class="new_line diff-line-num old" data-linenumber="2118" 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="LC2102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fgcp1opt</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2103" 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">
2103
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<td class="new_line diff-line-num old" data-linenumber="2118" 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="LC2103" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fgcp2opt</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2118
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<pre style="margin: 0;">+<span id="LC2118" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fgcp1opt</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fgcp2opt</span> <span class="p">);</span></span>
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2104
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<td class="new_line diff-line-num" data-linenumber="2120" 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">
2120
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<pre style="margin: 0;"> <span id="LC2120" class="line" lang="c"></span>
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2105
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<td class="new_line diff-line-num old" data-linenumber="2121" 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="LC2105" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="p">);</span></span>
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2106
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<td class="new_line diff-line-num old" data-linenumber="2121" 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="LC2106" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx1</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx1pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq1pt</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmx2</span><span class="o" style="font-weight: 600;">!=<span class="idiff left right">*</span></span><span class="n" style="color: #333;">cpmx2pt</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapfreq2pt</span> <span class="p">);</span></span>
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2107
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<td class="new_line diff-line-num" data-linenumber="2123" 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">
2123
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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2108
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<td class="new_line diff-line-num" data-linenumber="2124" 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">
2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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2109
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2125
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<pre style="margin: 0;"> <span id="LC2125" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; j<nalphabets; j++ ) </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">@@ -2124,16 +2140,24 @@ fprintf( stderr, "\n" );</td>
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2124
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2140
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<pre style="margin: 0;"> <span id="LC2140" class="line" lang="c"></span>
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2125
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2141
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<pre style="margin: 0;"> <span id="LC2141" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gt1bk</span> <span class="p">);</span></span>
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2126
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2142
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<pre style="margin: 0;"> <span id="LC2142" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gt2bk</span> <span class="p">);</span></span>
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2127
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<pre style="margin: 0;">-<span id="LC2127" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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2128
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<pre style="margin: 0;">-<span id="LC2128" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( cpmx1pt != cpmx1 ) </span></span>
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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0<span class="idiff left right"> // 2021/Jun/24</span></span></span>
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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( <span class="idiff left right">*</span>cpmx1pt != cpmx1 ) </span></span>
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2129
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2145
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<pre style="margin: 0;"> <span id="LC2145" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2130
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<pre style="margin: 0;">-<span id="LC2130" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxchild0\n" );</span></span>
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2131
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<pre style="margin: 0;">-<span id="LC2131" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FreeDoubleMtx( cpmxchild0 );</span></span>
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2146
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<pre style="margin: 0;">+<span id="LC2146" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( cpmxchild0 && *cpmxchild0 )</span></span>
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2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "freeing *cpmxchild0\n" );</span></span>
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2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FreeDoubleMtx( *cpmxchild0 );</span></span>
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2150
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<pre style="margin: 0;">+<span id="LC2150" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> *cpmxchild0 = NULL;</span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2132
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2133
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<pre style="margin: 0;">-<span id="LC2133" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( cpmx2pt != cpmx2 ) </span></span>
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2153
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<pre style="margin: 0;">+<span id="LC2153" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( <span class="idiff left right">*</span>cpmx2pt != cpmx2 ) </span></span>
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2134
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2154
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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2135
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<pre style="margin: 0;">-<span id="LC2135" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxchild1\n" );</span></span>
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2136
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<pre style="margin: 0;">-<span id="LC2136" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FreeDoubleMtx( cpmxchild1 );</span></span>
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2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( cpmxchild1 && *cpmxchild1 )</span></span>
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2156
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<pre style="margin: 0;">+<span id="LC2156" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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2157
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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "freeing *cpmxchild1\n" );</span></span>
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2158
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FreeDoubleMtx( *cpmxchild1 );</span></span>
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2159
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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> *cpmxchild1 = NULL;</span></span>
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2160
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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2137
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2161
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<pre style="margin: 0;"> <span id="LC2161" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2138
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2162
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<pre style="margin: 0;"> <span id="LC2162" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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2139
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2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#a0ceacde4b98f9b54a66b69e1010719564b2ba72"><strong>core/disttbfast.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1927" 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">@@ -1927,7 +1927,7 @@ static void *treebasethread( void *arg )</td>
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1927
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1927
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<pre style="margin: 0;"> <span id="LC1927" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ssi</span><span class="p">,</span> <span class="n" style="color: #333;">ssm</span><span class="p">,</span> <span class="n" style="color: #333;">bunbo</span><span class="p">;</span></span>
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1928
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1928
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<pre style="margin: 0;"> <span id="LC1928" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tm</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="p">;</span></span>
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1929
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1929
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<pre style="margin: 0;"> <span id="LC1929" 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;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1930
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<pre style="margin: 0;">-<span id="LC1930" 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;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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1931
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1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span><span class="p">;</span></span>
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1932
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="c"> <span class="n" style="color: #333;">ExtAnch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairanch</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1933
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2078" 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="2078" 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">@@ -2078,8 +2078,8 @@ static void *treebasethread( void *arg )</td>
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2078
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2078
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<pre style="margin: 0;"> <span id="LC2078" class="line" lang="c"></span>
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2079
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2079
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<pre style="margin: 0;"> <span id="LC2079" class="line" lang="c"></span>
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2080
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2080
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<pre style="margin: 0;"> <span id="LC2080" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "l=%d, dep[l].child0=%d, dep[l].child1=%d\n", l, dep[l].child0, dep[l].child1 );</span></span>
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2081
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<pre style="margin: 0;">-<span id="LC2081" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p"><span class="idiff right">]</span>;</span></span>
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2082
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<pre style="margin: 0;">-<span id="LC2082" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p"><span class="idiff right">]</span>;</span></span>
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2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p">;</span></span>
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2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p">;</span></span>
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2083
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2083
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<pre style="margin: 0;"> <span id="LC2083" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "cpmxchild0=%p, cpmxchild1=%p\n", cpmxchild0, cpmxchild1 );</span></span>
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2084
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2084
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<pre style="margin: 0;"> <span id="LC2084" class="line" lang="c"></span>
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2085
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2085
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<pre style="margin: 0;"> <span id="LC2085" 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">@@ -2259,7 +2259,7 @@ static void *treebasethread( void *arg )</td>
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2259
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2259
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<pre style="margin: 0;"> <span id="LC2259" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2260
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2260
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<pre style="margin: 0;"> <span id="LC2260" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'M'</span> <span class="p">):</span></span>
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2261
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2261
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<pre style="margin: 0;"> <span id="LC2261" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"m"</span> <span class="p">);</span></span>
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2262
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<pre style="margin: 0;">-<span id="LC2262" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2262
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<pre style="margin: 0;">+<span id="LC2262" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2263
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2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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2264
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2264
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<pre style="margin: 0;"> <span id="LC2264" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MSalignmm</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2265" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</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">@@ -2284,7 +2284,7 @@ static void *treebasethread( void *arg )</td>
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2286" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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<pre style="margin: 0;">-<span id="LC2287" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2288" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="n" style="color: #333;">penalty_ex</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dumdb</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2289" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</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">@@ -2420,7 +2420,7 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,</td>
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<pre style="margin: 0;"> <span id="LC2420" 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;">alreadyaligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2421
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<pre style="margin: 0;"> <span id="LC2421" 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;">dynamicmtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2422
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2422
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<pre style="margin: 0;"> <span id="LC2422" 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;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2423" 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;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2423" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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2424
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<pre style="margin: 0;"> <span id="LC2424" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2425" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">oscore</span><span class="p">,</span> <span class="n" style="color: #333;">nscore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2426" class="line" lang="c"> <span class="n" style="color: #333;">ExtAnch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairanch</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">@@ -2606,7 +2606,7 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,</td>
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2606
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2606
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<pre style="margin: 0;"> <span id="LC2606" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2607
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2607
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<pre style="margin: 0;"> <span id="LC2607" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'M'</span> <span class="p">):</span></span>
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2608
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2608
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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"m"</span> <span class="p">);</span></span>
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2609
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<pre style="margin: 0;">-<span id="LC2609" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2609
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<pre style="margin: 0;">+<span id="LC2609" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2610
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2610
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<pre style="margin: 0;"> <span id="LC2610" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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2611
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2611
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<pre style="margin: 0;"> <span id="LC2611" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MSalignmm</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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2612
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2612
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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</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">@@ -2630,7 +2630,7 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,</td>
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2630
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2630
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<pre style="margin: 0;"> <span id="LC2630" class="line" lang="c"> <span class="p">}</span></span>
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2631
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2631
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<pre style="margin: 0;"> <span id="LC2631" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2632
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2632
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<pre style="margin: 0;"> <span id="LC2632" class="line" lang="c"> <span class="p">{</span></span>
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2633
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<pre style="margin: 0;">-<span id="LC2633" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2633
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<pre style="margin: 0;">+<span id="LC2633" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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2634
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\n\n %d - %d (%d x %d) : \n", topol[l][0][0], topol[l][1][0], clus1, clus2 );</span></span>
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<pre style="margin: 0;"> <span id="LC2635" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="n" style="color: #333;">penalty_ex</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dumdb</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2636" 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">@@ -2748,7 +2748,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char</td>
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<pre style="margin: 0;"> <span id="LC2748" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tm</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="p">;</span></span>
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2749
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<pre style="margin: 0;"> <span id="LC2749" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapmaplen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2750" 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;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2751
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<pre style="margin: 0;">-<span id="LC2751" 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;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2751" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2752" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2753" class="line" lang="c"> <span class="n" style="color: #333;">ExtAnch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairanch</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2754" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</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">@@ -2808,8 +2808,8 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char</td>
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<pre style="margin: 0;"> <span id="LC2808" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( " at the beginning of the loop, clus1,clus2=%d,%d\n", clus1, clus2 );</span></span>
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2809
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<pre style="margin: 0;"> <span id="LC2809" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2810" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "l=%d, dep[l].child0=%d, dep[l].child1=%d\n", l, dep[l].child0, dep[l].child1 );</span></span>
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<pre style="margin: 0;">-<span id="LC2811" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC2812" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC2811" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p">;</span></span>
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2812
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<pre style="margin: 0;">+<span id="LC2812" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p">;</span></span>
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2813
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2813
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<pre style="margin: 0;"> <span id="LC2813" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "cpmxchild0=%p, cpmxchild1=%p\n", cpmxchild0, cpmxchild1 );</span></span>
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2814
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2814
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<pre style="margin: 0;"> <span id="LC2814" class="line" lang="c"></span>
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2815
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2815
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<pre style="margin: 0;"> <span id="LC2815" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3075" 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="3075" 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">@@ -3075,7 +3075,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char</td>
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3075
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3075
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<pre style="margin: 0;"> <span id="LC3075" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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3076
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3076
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<pre style="margin: 0;"> <span id="LC3076" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'M'</span> <span class="p">):</span></span>
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3077
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3077
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<pre style="margin: 0;"> <span id="LC3077" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"m"</span> <span class="p">);</span></span>
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3078
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<td class="new_line diff-line-num old" data-linenumber="3078" 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="LC3078" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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3078
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<pre style="margin: 0;">+<span id="LC3078" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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3079
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3079
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<pre style="margin: 0;"> <span id="LC3079" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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3080
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3080
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<pre style="margin: 0;"> <span id="LC3080" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MSalignmm</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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3081
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3081
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<pre style="margin: 0;"> <span id="LC3081" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3099" 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">@@ -3099,7 +3099,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char</td>
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3099
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3099
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<pre style="margin: 0;"> <span id="LC3099" class="line" lang="c"> <span class="p">}</span></span>
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3100
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3100
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<pre style="margin: 0;"> <span id="LC3100" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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3101
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3101
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<pre style="margin: 0;"> <span id="LC3101" class="line" lang="c"> <span class="p">{</span></span>
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3102
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<pre style="margin: 0;">-<span id="LC3102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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3102
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<pre style="margin: 0;">+<span id="LC3102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</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">cpmxchild0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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3103
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<pre style="margin: 0;"> <span id="LC3103" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\n\n %d - %d (%d x %d) : \n", topol[l][0][0], topol[l][1][0], clus1, clus2 );</span></span>
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3104
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3104
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<pre style="margin: 0;"> <span id="LC3104" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="n" style="color: #333;">penalty_ex</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dumdb</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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3105
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3105
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<pre style="margin: 0;"> <span id="LC3105" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4766" 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">@@ -4766,12 +4766,27 @@ int disttbfast( int ngui, int lgui, char **namegui, char **seqgui, int argc, cha</td>
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4766
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4766
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<pre style="margin: 0;"> <span id="LC4766" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[njob-1] ); topol[njob-1]=NULL;</span></span>
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4767
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4767
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<pre style="margin: 0;"> <span id="LC4767" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol ); topol=NULL;</span></span>
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4768
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4768
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<pre style="margin: 0;"> <span id="LC4768" class="line" lang="c"> <span class="n" style="color: #333;">FreeIntCub</span><span class="p">(</span> <span class="n" style="color: #333;">topol</span> <span class="p">);</span> <span class="n" style="color: #333;">topol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4769
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<pre style="margin: 0;">+<span id="LC4769" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1 // 2021/Jun/24</span></span>
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4770
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<pre style="margin: 0;">+<span id="LC4770" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// nakutemo yoi</span></span>
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4771
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<pre style="margin: 0;">+<span id="LC4771" class="line" lang="c"> <span class="p">{</span></span>
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4772
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<pre style="margin: 0;">+<span id="LC4772" 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;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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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4773
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<pre style="margin: 0;">+<span id="LC4773" class="line" lang="c"> <span class="p">{</span></span>
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4774
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<pre style="margin: 0;">+<span id="LC4774" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">)</span> </span>
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4775
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<pre style="margin: 0;">+<span id="LC4775" class="line" lang="c"> <span class="p">{</span></span>
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4776
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<pre style="margin: 0;">+<span id="LC4776" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxhist[%d]\n", i );</span></span>
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<pre style="margin: 0;">+<span id="LC4777" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4778
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<pre style="margin: 0;">+<span id="LC4778" class="line" lang="c"> <span class="p">}</span></span>
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4779
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<pre style="margin: 0;">+<span id="LC4779" class="line" lang="c"> <span class="p">}</span></span>
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4780
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<pre style="margin: 0;">+<span id="LC4780" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4781
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<pre style="margin: 0;">+<span id="LC4781" class="line" lang="c"> <span class="p">}</span></span>
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4782
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<pre style="margin: 0;">+<span id="LC4782" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4769
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4783
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<pre style="margin: 0;"> <span id="LC4783" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">)</span> </span>
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4770
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4784
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<pre style="margin: 0;"> <span id="LC4784" class="line" lang="c"> <span class="p">{</span></span>
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4771
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4785
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<pre style="margin: 0;"> <span id="LC4785" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxhist[njob-2]\n" );</span></span>
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4772
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4786
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<pre style="margin: 0;"> <span id="LC4786" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4773
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4787
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<pre style="margin: 0;"> <span id="LC4787" class="line" lang="c"> <span class="p">}</span></span>
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4774
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4788
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<pre style="margin: 0;"> <span id="LC4788" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4789" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4790
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<pre style="margin: 0;"> <span id="LC4790" class="line" lang="c"></span>
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4776
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4791
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<pre style="margin: 0;"> <span id="LC4791" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">memhist</span> <span class="p">);</span> <span class="n" style="color: #333;">memhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4792" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "after freeing topol, " );</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#58e2e0082bb4ca16bc55a2289e58d89f679360a0"><strong>core/functions.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,13 +141,13 @@ extern void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, d</td>
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<pre style="margin: 0;"> <span id="LC141" 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;">blockAlign3</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;">cut1</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;">cut2</span><span class="p">,</span> <span class="n" style="color: #333;">Segment</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seg1</span><span class="p">,</span> <span class="n" style="color: #333;">Segment</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seg2</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;">ocrossscore</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;">ncut</span> <span class="p">);</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">imp_match_out_scD</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j1</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">imp_match_init_strictD</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;">imp</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;">int</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth2</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff1kozo</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;">eff2kozo</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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">swaplist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">forscore</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;">memlist1</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;">memlist2</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;">uselh</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;">seedinlh1</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;">seedinlh2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nodeid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfiles</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalignmm</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;">n_dynamicmtx</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</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;">cpmxchild0</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;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalignmm</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;">n_dynamicmtx</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalignmm_variousdist</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;">pairoffset</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;">matrices</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;">dummtx</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">eff1s</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;">eff2s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">Lalignmm_hmout</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</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="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">map</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">Lalign2m2m_hmout</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;">seq1</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;">seq2</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;">seq1r</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;">seq2r</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;">dir1</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;">dir2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</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="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">map</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">MSalign11</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;">seq1</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;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="p">);</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//extern double rnalocal( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, RNApair **pair );</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align</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;">scoringmtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_ex</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">gs1</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;">gs2</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;">ge1</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;">ge2</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstmem</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">calledby</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;">cpmxchild0</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;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align</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;">scoringmtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_ex</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">gs1</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;">gs2</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;">ge1</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;">ge2</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstmem</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">calledby</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**<span class="idiff left">*</span></span><span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff right">*</span>**</span><span class="n" style="color: #333;">cpmxchild1</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;">cpmxresult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align_variousdist</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;">which</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;">scoringmatrices</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;">dummtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">penalty_ex</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">eff1s</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;">eff2s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">gs1</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;">gs2</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;">ge1</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;">ge2</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">headgp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailgp</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">A__align_gapmap</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">icyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jcyc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">constraint</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;">impmatch</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;">gapmap1</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;">gapmap2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">translate_and_Calign</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;">mseq1</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;">mseq2</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;">effarr1</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;">effarr2</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;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="408" 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="408" 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">@@ -408,7 +408,7 @@ extern double distcompact( int len1, int len2, int *table1, int *point2, int ss1</td>
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408
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">distcompact_msa</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;">seq1</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;">seq2</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;">skiptable1</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;">skiptable2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ss1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ss2</span> <span class="p">);</span></span>
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409
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409
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<pre style="margin: 0;"> <span id="LC409" 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;">fillimp</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;">impmtx</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;">imp</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;">int</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth2</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff1_kozo</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_kozo</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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">swaplist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">forscore</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;">orinum1</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;">orinum2</span> <span class="p">);</span></span>
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410
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410
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<pre style="margin: 0;"> <span id="LC410" 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;">fillimp_file</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;">impmtx</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;">imp</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;">int</span> <span class="n" style="color: #333;">lgth1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth2</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;">seq1</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;">seq2</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff1_kozo</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_kozo</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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">swaplist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">forscore</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;">orinum1</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;">orinum2</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;">uselh</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;">seedinlh1</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;">seedinlh2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nodeid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfiles</span> <span class="p">);</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</span> <span class="p">);</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</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">double</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">expdist</span></span> <span class="p">);</span></span>
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412
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<pre style="margin: 0;"> <span id="LC412" 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="nf" style="color: #900; font-weight: 600;">creverse</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">f</span> <span class="p">);</span></span>
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413
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef mingw</span></span>
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414
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414
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<pre style="margin: 0;"> <span id="LC414" 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;">setstacksize</span><span class="p">(</span> <span class="n" style="color: #333;">rlim_t</span> <span class="p">);</span></span>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash </span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">er</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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3
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<td class="new_line diff-line-num" data-linenumber="3" 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">
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;">"v7.48<span class="idiff left">1</span> (2021/<span class="idiff right">May/26</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;">"v7.48<span class="idiff left">6</span> (2021/<span class="idiff right">Jul/19</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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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="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="294" 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">@@ -294,6 +294,7 @@ enrich=0 # ato de kezuru</td>
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294
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="shell"><span class="nv" style="color: #008080;">enrichseq</span><span class="o" style="font-weight: 600;">=</span>0 <span class="c" style="color: #998; font-style: italic;"># ato de kezuru</span></span>
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295
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="shell"><span class="nv" style="color: #008080;">enrichstr</span><span class="o" style="font-weight: 600;">=</span>0 <span class="c" style="color: #998; font-style: italic;"># ato de kezuru</span></span>
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296
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="shell"><span class="nv" style="color: #008080;">seektarget</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span> <span class="c" style="color: #998; font-style: italic;"># ato de kezuru</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="shell"><span class="nv" style="color: #008080;">dashserver</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"https://sysimm.org/dash/REST1.0/"</span></span>
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297
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="shell"><span class="nv" style="color: #008080;">newdash</span><span class="o" style="font-weight: 600;">=</span>0</span>
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298
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="shell"><span class="nv" style="color: #008080;">newdash_originalsequenceonly</span><span class="o" style="font-weight: 600;">=</span>0</span>
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299
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="shell"><span class="nv" style="color: #008080;">exclude_ho</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="952" 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="953" 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">@@ -952,6 +953,9 @@ if [ $# -gt 0 ]; then</td>
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952
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">newdash</span><span class="o" style="font-weight: 600;">=</span>1</span>
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953
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="shell"> <span class="nv" style="color: #008080;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"global"</span> <span class="c" style="color: #998; font-style: italic;"># can be override</span></span>
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954
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="shell"> <span class="nv" style="color: #008080;">iterate</span><span class="o" style="font-weight: 600;">=</span>3 <span class="c" style="color: #998; font-style: italic;"># can be override</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--dashserver"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">shift</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">dashserver</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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955
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--originalseqonly"</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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956
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">newdash_originalsequenceonly</span><span class="o" style="font-weight: 600;">=</span>1</span>
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957
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--excludehomologs"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># works with --dash only</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">@@ -2369,7 +2373,7 @@ $ownlist"</td>
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2369
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2373
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<pre style="margin: 0;"> <span id="LC2373" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2370
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2374
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<pre style="margin: 0;"> <span id="LC2374" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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2371
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2375
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<pre style="margin: 0;"> <span id="LC2375" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Calling DASH (https://sysimm.org/dash/)"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2372
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<pre style="margin: 0;">-<span id="LC2372" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;">-i</span> dashin <span class="nt" style="color: #000080;">-sequences</span> dashsequences <span class="nt" style="color: #000080;">-hat3</span> hat3.seed 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;"><span class="idiff left">-url</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$dashserver</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="nt" style="color: #000080;">-i</span> dashin <span class="nt" style="color: #000080;">-sequences</span> dashsequences <span class="nt" style="color: #000080;">-hat3</span> hat3.seed 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2373
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2377
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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="shell"> <span class="nv" style="color: #008080;">dashres</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$?</span><span class="s2" style="color: #d14;">"</span></span>
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2374
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2378
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<pre style="margin: 0;"> <span id="LC2378" 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;">$dashres</span> <span class="nt" style="color: #000080;">-ne</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2375
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2379
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<pre style="margin: 0;"> <span id="LC2379" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Error in DASH"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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<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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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.48<span class="idiff left right">1</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 "7.48<span class="idiff left right">6</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="LC41" class="line" lang="c"></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">@@ -520,7 +520,10 @@ void FreeDoubleMtx( double **mtx )</td>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC522" 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;">mtx</span><span class="p">[</span><span class="n" style="color: #333;">i</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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<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;">FreeDoubleVec</span><span class="p">(</span> <span class="n" style="color: #333;">mtx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">mtx</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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mtx</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC529" 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">@@ -71,6 +71,7 @@ typedef struct _thread_arg</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" 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;">targetmap</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" 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;">expdist</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mutex_counter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">pthread_mutex_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mutex_stdout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">thread_arg_t</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1973" 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">@@ -1972,6 +1973,7 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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1972
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="c"> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lastresx</span><span class="p">;</span></span>
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1973
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1974
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<pre style="margin: 0;"> <span id="LC1974" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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1974
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1975
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<pre style="margin: 0;"> <span id="LC1975" 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;">targetmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">targetmap</span><span class="p">;</span></span>
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1976
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<pre style="margin: 0;">+<span id="LC1976" 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;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targ</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">expdist</span><span class="p">;</span></span>
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1975
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1977
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<pre style="margin: 0;"> <span id="LC1977" class="line" lang="c"></span>
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1976
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1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "thread %d start!\n", thread_no );</span></span>
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1977
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2137" 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="2139" 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">@@ -2137,7 +2139,10 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2137
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2139
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<pre style="margin: 0;"> <span id="LC2139" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2138
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2140
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<pre style="margin: 0;"> <span id="LC2140" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2139
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2141
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<pre style="margin: 0;"> <span id="LC2141" class="line" lang="c"> <span class="p">{</span></span>
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2140
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<pre style="margin: 0;">-<span id="LC2140" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2141
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2146
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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">scoreoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</span> <span class="p">)</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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2142
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="c"> <span class="p">{</span></span>
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2143
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2192" 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="2197" 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">@@ -2192,8 +2197,11 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2192
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2197
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2193
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2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2194
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2199
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<pre style="margin: 0;"> <span id="LC2199" class="line" lang="c"> <span class="p">{</span></span>
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2195
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<pre style="margin: 0;">-<span id="LC2195" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2196
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<pre style="margin: 0;">-<span id="LC2196" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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2197
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2205
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<pre style="margin: 0;"> <span id="LC2205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2198
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2206
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="c"> <span class="p">{</span></span>
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2199
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2207
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<pre style="margin: 0;"> <span id="LC2207" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2204" 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="2212" 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">@@ -2204,6 +2212,7 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2204
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2212
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<pre style="margin: 0;"> <span id="LC2212" class="line" lang="c"> <span class="p">}</span></span>
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2205
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// pscore = (double)naivepairscore11( *mseq1, *mseq2, 0.0 );</span></span>
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2206
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="c"> <span class="p">}</span></span>
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2215
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<pre style="margin: 0;">+<span id="LC2215" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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2207
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2216
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<pre style="margin: 0;"> <span id="LC2216" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2208
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2217
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<pre style="margin: 0;"> <span id="LC2217" class="line" lang="c"> <span class="p">}</span></span>
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2209
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2239" 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">@@ -2230,7 +2239,10 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2230
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2239
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<pre style="margin: 0;"> <span id="LC2239" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2231
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2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2232
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2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="c"> <span class="p">{</span></span>
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2233
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<pre style="margin: 0;">-<span id="LC2233" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2234
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2235
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="c"> <span class="p">{</span></span>
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2236
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2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></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>
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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">@@ -2373,7 +2385,7 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai.</td>
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2373
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2385
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="c"><span class="p">}</span></span>
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2374
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2386
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2375
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2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="c"></span>
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2376
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<pre style="margin: 0;">-<span id="LC2376" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairalign</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;">name</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;">nlen</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">aseq</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;">dseq</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;">thereisxineachseq</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;">mseq1</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;">mseq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairalign</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;">name</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;">nlen</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">aseq</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;">dseq</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;">thereisxineachseq</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;">mseq1</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;">mseq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">Lastresx</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">lastresx</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</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">expdist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span> <span class="p">)</span></span>
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2377
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2389
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<pre style="margin: 0;"> <span id="LC2389" class="line" lang="c"><span class="p">{</span></span>
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2378
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2390
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<pre style="margin: 0;"> <span id="LC2390" 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;">ilim</span><span class="p">,</span> <span class="n" style="color: #333;">jst</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="p">;</span></span>
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2379
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2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">off1</span><span class="p">,</span> <span class="n" style="color: #333;">off2</span><span class="p">,</span> <span class="n" style="color: #333;">dum1</span><span class="p">,</span> <span class="n" style="color: #333;">dum2</span><span class="p">,</span> <span class="n" style="color: #333;">thereisx</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2616" 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="2628" 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">@@ -2616,6 +2628,7 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2616
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2628
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<pre style="margin: 0;"> <span id="LC2628" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bpp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpp</span><span class="p">;</span> </span>
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<td class="old_line diff-line-num" data-linenumber="2617" 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">
2617
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<td class="new_line diff-line-num" data-linenumber="2629" 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">
2629
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<pre style="margin: 0;"> <span id="LC2629" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">lastresx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastresx</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2618" 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">
2618
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2630
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<pre style="margin: 0;"> <span id="LC2630" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alloclen</span><span class="p">;</span></span>
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2631
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<pre style="margin: 0;">+<span id="LC2631" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">;</span></span>
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2619
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2632
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<pre style="margin: 0;"> <span id="LC2632" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">targetmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targetmap</span><span class="p">;</span></span>
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2620
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2633
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<pre style="margin: 0;"> <span id="LC2633" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mutex_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_counter</span><span class="p">;</span></span>
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2621
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2634
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="c"> <span class="n" style="color: #333;">targ</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mutex_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_stdout</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2724" 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="2737" 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">@@ -2724,8 +2737,12 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2724
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2737
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<pre style="margin: 0;"> <span id="LC2737" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2725
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2738
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<pre style="margin: 0;"> <span id="LC2738" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2726
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2739
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<pre style="margin: 0;"> <span id="LC2739" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2727" 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">
2727
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<td class="new_line diff-line-num old" data-linenumber="2740" 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="LC2727" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2740
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<pre style="margin: 0;">+<span id="LC2740" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2741
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<pre style="margin: 0;">+<span id="LC2741" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2742
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<pre style="margin: 0;">+<span id="LC2742" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2743
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<pre style="margin: 0;">+<span id="LC2743" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2728
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2744
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<pre style="margin: 0;"> <span id="LC2744" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dist = score2dist( L__align11_noalign( n_dis_consweight_multi, distseq1, distseq2 ), selfscore[i], selfscore[j] ); // 2014/Feb/20</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2745
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<pre style="margin: 0;">+<span id="LC2745" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "dist(%d,%d)=%f\n", i, j, dist );</span></span>
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2729
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<td class="new_line diff-line-num" data-linenumber="2746" 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">
2746
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<pre style="margin: 0;"> <span id="LC2746" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2730
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2747
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<pre style="margin: 0;"> <span id="LC2747" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2731" 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">
2731
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<td class="new_line diff-line-num" data-linenumber="2748" 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">
2748
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<pre style="margin: 0;"> <span id="LC2748" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2762" 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="2779" 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">@@ -2762,7 +2779,10 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2762
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2779
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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2763
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2780
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<pre style="margin: 0;"> <span id="LC2780" class="line" lang="c"> <span class="p">{</span></span>
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2764
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<td class="new_line diff-line-num" data-linenumber="2781" 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">
2781
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<pre style="margin: 0;"> <span id="LC2781" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "dist = %f\n", score2dist( pscore, selfscore[i], selfscore[j] ) );</span></span>
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2765
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<td class="new_line diff-line-num old" data-linenumber="2782" 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="LC2765" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2782
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<pre style="margin: 0;">+<span id="LC2782" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2783
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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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<td class="new_line diff-line-num new" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2784
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<pre style="margin: 0;">+<span id="LC2784" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2785
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<pre style="margin: 0;">+<span id="LC2785" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2766
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2786
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<pre style="margin: 0;"> <span id="LC2786" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</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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2767
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2787
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<pre style="margin: 0;"> <span id="LC2787" class="line" lang="c"> <span class="p">{</span></span>
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2768
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2788
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<pre style="margin: 0;"> <span id="LC2788" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2806" 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="2826" 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">@@ -2806,7 +2826,10 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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2806
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2826
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<pre style="margin: 0;"> <span id="LC2826" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2807
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2827
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<pre style="margin: 0;"> <span id="LC2827" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</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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2808
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2828
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<pre style="margin: 0;"> <span id="LC2828" class="line" lang="c"> <span class="p">{</span></span>
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2809
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<td class="new_line diff-line-num old" data-linenumber="2829" 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="LC2809" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2829
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<pre style="margin: 0;">+<span id="LC2829" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> </span>
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2830
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<pre style="margin: 0;">+<span id="LC2830" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expdist</span><span class="p">[</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>
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2831
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<pre style="margin: 0;">+<span id="LC2831" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2832
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<pre style="margin: 0;">+<span id="LC2832" class="line" lang="c"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score2dist</span><span class="p">(</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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2810
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<td class="new_line diff-line-num" data-linenumber="2833" 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">
2833
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<pre style="margin: 0;"> <span id="LC2833" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">scoreoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist2offset</span><span class="p">(</span> <span class="n" style="color: #333;">dist</span> <span class="p">)</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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2811
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2834
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<pre style="margin: 0;"> <span id="LC2834" class="line" lang="c"> <span class="p">{</span></span>
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2812
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2835
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<pre style="margin: 0;"> <span id="LC2835" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dist</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// upgma ni awaseru.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3065" 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="3088" 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">@@ -3065,7 +3088,7 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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3065
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3088
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<pre style="margin: 0;"> <span id="LC3088" class="line" lang="c"><span class="p">}</span></span>
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3089
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<pre style="margin: 0;"> <span id="LC3089" class="line" lang="c"></span>
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3067
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3090
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<pre style="margin: 0;"> <span id="LC3090" class="line" lang="c"></span>
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3068
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<pre style="margin: 0;">-<span id="LC3068" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</span> <span class="p">)</span></span>
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3091
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<pre style="margin: 0;">+<span id="LC3091" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pairlocalalign</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngui</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgui</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;">namegui</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;">seqgui</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;">distancemtx</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;">localhomtable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</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">double</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">expdist</span></span> <span class="p">)</span></span>
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3069
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3092
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<pre style="margin: 0;"> <span id="LC3092" class="line" lang="c"><span class="p">{</span></span>
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3070
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3093
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<pre style="margin: 0;"> <span id="LC3093" 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;">nlen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thereisxineachseq</span><span class="p">;</span></span>
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3071
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3094
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<pre style="margin: 0;"> <span id="LC3094" class="line" lang="c"> <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;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3211" 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="3234" 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">@@ -3211,8 +3234,7 @@ int pairlocalalign( int ngui, int lgui, char **namegui, char **seqgui, double **</td>
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3211
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3234
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<pre style="margin: 0;"> <span id="LC3234" class="line" lang="c"></span>
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3212
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3235
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<pre style="margin: 0;"> <span id="LC3235" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// writePre( njob, name, nlen, seq, 0 );</span></span>
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3213
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3236
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<pre style="margin: 0;"> <span id="LC3236" class="line" lang="c"></span>
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3214
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<pre style="margin: 0;">-<span id="LC3214" class="line" lang="c"></span>
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3215
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<pre style="margin: 0;">-<span id="LC3215" class="line" lang="c"></span>
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3237
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<pre style="margin: 0;">+<span id="LC3237" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//reporterr( "expdist=%p\n", expdist );</span></span>
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3216
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3238
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<pre style="margin: 0;"> <span id="LC3238" class="line" lang="c"></span>
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3217
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3239
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<pre style="margin: 0;"> <span id="LC3239" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'p'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">scoremtx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nblosum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// protein, not text. hitsuyou?</span></span>
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3218
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3240
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<pre style="margin: 0;"> <span id="LC3240" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3232" 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="3254" 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">@@ -3232,7 +3254,7 @@ int pairlocalalign( int ngui, int lgui, char **namegui, char **seqgui, double **</td>
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3232
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3254
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<pre style="margin: 0;"> <span id="LC3254" class="line" lang="c"> <span class="p">}</span></span>
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3233
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3255
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<pre style="margin: 0;"> <span id="LC3255" class="line" lang="c"> <span class="p">}</span></span>
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3234
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3256
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<pre style="margin: 0;"> <span id="LC3256" class="line" lang="c"></span>
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3235
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<pre style="margin: 0;">-<span id="LC3235" class="line" lang="c"> <span class="n" style="color: #333;">pairalign</span><span class="p">(</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">dseq</span><span class="p">,</span> <span class="n" style="color: #333;">thereisxineachseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">lastresx</span><span class="p">,</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">ngui</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3257
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<pre style="margin: 0;">+<span id="LC3257" class="line" lang="c"> <span class="n" style="color: #333;">pairalign</span><span class="p">(</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">bseq</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">dseq</span><span class="p">,</span> <span class="n" style="color: #333;">thereisxineachseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="n" style="color: #333;">lastresx</span><span class="p">,</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">expdist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ngui</span> <span class="p">);</span></span>
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3236
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3258
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<pre style="margin: 0;"> <span id="LC3258" class="line" lang="c"></span>
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3237
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3259
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<pre style="margin: 0;"> <span id="LC3259" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">trap_g</span><span class="p">,</span> <span class="s" style="color: #d14;">"done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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3238
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3260
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<pre style="margin: 0;"> <span id="LC3260" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if DEBUG</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#6f036ff28d08d3462cd8f0b59de73fb1b1636ed2"><strong>core/pairlocalalignmain.c</strong></a>
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1
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1
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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;">argv</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">GUI_CANCEL</span> <span class="p">)</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// treeout de goto chudan wo riyousuru</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#b3a870840642b1943f3cb55ad3a88066fdb6d139"><strong>core/serial.c</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">treebase</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;">nlen</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;">aseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nadd</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;">mergeoralign</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;">mseq1</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;">mseq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="n" style="color: #333;">Treedep</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dep</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;">memhist</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;">cpmxhist</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;">effarr</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;">newdistmtx</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;">selfscore</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;">alloclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">callback</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">len1</span><span class="p">,</span> <span class="n" style="color: #333;">len2</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">immin</span><span class="p">,</span> <span class="n" style="color: #333;">immax</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len1nocommongap</span><span class="p">,</span> <span class="n" style="color: #333;">len2nocommongap</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"> <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="n" style="color: #333;">clus2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pscore</span><span class="p">,</span> <span class="n" style="color: #333;">tscore</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"> <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;">indication1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">indication2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC8" 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;">effarr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC9" 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;">effarr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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;">fftlog</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// fixed at 2006/07/26</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// double dumfl = 0.0;</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dumdb</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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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ffttry</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="n" style="color: #333;">m2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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;">gaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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;">gapmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC17" 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;">alreadyaligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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;">dynamicmtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ssi</span><span class="p">,</span> <span class="n" style="color: #333;">ssm</span><span class="p">,</span> <span class="n" style="color: #333;">bunbo</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tm</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapmaplen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC22" 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;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" 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;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" 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;">skiptable1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">skiptable2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> int i, j;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">effarr1</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">effarr1</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;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">effarr2</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;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">indication1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharVec</span><span class="p">(</span> <span class="mi" style="color: #099;">150</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">indication2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharVec</span><span class="p">(</span> <span class="mi" style="color: #099;">150</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">fftlog</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;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">gaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="p">);</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">gapmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">alreadyaligned</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;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">dynamicmtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">nalphabets</span><span class="p">,</span> <span class="n" style="color: #333;">nalphabets</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</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="p">),</span> <span class="mi" style="color: #099;">2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nadd</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 class="n" style="color: #333;">alreadyaligned</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" 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="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nadd</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;">njob</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 class="n" style="color: #333;">alreadyaligned</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">callback</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">callback</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="s" style="color: #d14;">"Progressive alignment"</span> <span class="p">)</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">chudan_tbfast</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">l</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;">l</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">njob</span><span class="p">;</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 // chain you</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[0][0] = -1;</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[1][0] = -1;</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> clus1 = 1;// chain ni hitsuyou</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC64" 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="LC65" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<njob; i++ )</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "TBFAST effarr[%d] = %f\n", i, effarr[i] );</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// writePre( njob, name, nlen, aseq, 0 );</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">tscore</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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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">l</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;">l</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="p">{</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">topol</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">m2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">topol</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">][</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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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( " at the beginning of the loop, clus1,clus2=%d,%d\n", clus1, clus2 );</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "l=%d, dep[l].child0=%d, dep[l].child1=%d\n", l, dep[l].child0, dep[l].child1 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="82" 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">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="83" 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">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p">];</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "cpmxchild0=%p, cpmxchild1=%p\n", cpmxchild0, cpmxchild1 );</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( l > 0 && dep[l].child0 == l-1 && dep[l].child1 == -1 && dep[dep[l].child0].child1 == -1 )</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[0][clus1] = topol[l-1][1][0];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="90" 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">
90
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC90" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[0][clus1+1] = -1;</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[1][0] = topol[l][1][0];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="93" 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">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[1][1] = -1;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> else</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[0][0] = -1;</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> posinmem = topolorderz( localmem[0], topol, dep, l, 0 ) - localmem[0];</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> localmem[1][0] = -1;</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> posinmem = topolorderz( localmem[1], topol, dep, l, 1 ) - localmem[1];</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#else</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="p">{</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">),</span> <span class="mi" style="color: #099;">2</span> <span class="p">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" 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">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</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>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">clus1</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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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="p">}</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p">];</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intlen</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="p">}</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" 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">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">),</span> <span class="mi" style="color: #099;">2</span> <span class="p">);</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="119" 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">
119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</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>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">clus2</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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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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123
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC123" class="line" lang="c"> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="125" 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">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intlen</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="126" 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">
126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="p">}</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="128" 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">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">njob</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="old_line diff-line-num old" data-linenumber="129" 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">
129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="130" 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">
130
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC130" class="line" lang="c"> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">),</span> <span class="n" style="color: #333;">clus1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clus2</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="131" 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">
131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">intcpy</span><span class="p">(</span> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">],</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" 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">
132
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC132" class="line" lang="c"> <span class="n" style="color: #333;">intcpy</span><span class="p">(</span> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="133" 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">
133
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC133" class="line" lang="c"> <span class="n" style="color: #333;">memhist</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">][</span><span class="n" style="color: #333;">clus1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clus2</span><span class="p">]</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>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"> <span class="p">}</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="old_line diff-line-num old" data-linenumber="136" 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">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="137" 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">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="138" 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">
138
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC138" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="139" 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">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "SKIP!\n" );</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l][0] ); topol[l][0] = NULL;</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l][1] ); topol[l][1] = NULL;</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l] ); topol[l] = NULL;</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="p">}</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\ndistfromtip = %f\n", dep[l].distfromtip );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="147" 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">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="148" 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">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">makedynamicmtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">,</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">distfromtip</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="149" 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">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">dynamicmtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_dis_consweight_multi</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// makedynamicmtx( dynamicmtx, n_dis_consweight_multi, ( dep[l].distfromtip - 0.2 ) * 3 );</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">len1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">aseq</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="p">);</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">len2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">aseq</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="p">);</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len2</span> <span class="p">)</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="p">{</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Reallocating.."</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="159" 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">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">len1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len2</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="160" 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">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">ReallocateCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span> <span class="p">);</span> </span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">gaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</span><span class="p">(</span> <span class="n" style="color: #333;">gaplen</span><span class="p">,</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">)</span> <span class="p">);</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplen</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"> <span class="p">{</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"Cannot realloc gaplen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="p">}</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">gapmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</span><span class="p">(</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">)</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="168" 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">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapmap</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="169" 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">
169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="p">{</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"Cannot realloc gapmap</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="171" 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">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="p">}</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"done. *alloclen = %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="p">);</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1 // CHUUI@@@@</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" 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">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastconjuction_noname</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">indication1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orieff1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="178" 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">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastconjuction_noname</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">indication2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="old_line diff-line-num old" data-linenumber="180" 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">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastconjuction_noname</span><span class="p">(</span> <span class="n" style="color: #333;">topol</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">indication1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastconjuction_noname</span><span class="p">(</span> <span class="n" style="color: #333;">topol</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr</span><span class="p">,</span> <span class="n" style="color: #333;">indication2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// clus1 = fastconjuction_noweight( topol[l][0], aseq, mseq1, effarr1, indication1 );</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// clus2 = fastconjuction_noweight( topol[l][1], aseq, mseq2, effarr2, indication2 );</span></span>
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<pre style="margin: 0;">-<span id="LC184" 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="LC195" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="p">{</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">newgapstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"="</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">newgapstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">len1nocommongap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len1</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">len2nocommongap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// nai</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">findcommongaps</span><span class="p">(</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap</span> <span class="p">);</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">commongappick</span><span class="p">(</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span> <span class="p">);</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">len2nocommongap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">mseq2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c"> <span class="p">}</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" 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;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span> <span class="p">)</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"> <span class="p">{</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">findcommongaps</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap</span> <span class="p">);</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">commongappick</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span> <span class="p">);</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">len1nocommongap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="p">}</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) </span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( mseq1[i] ) != len1 ) </span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "i = %d / %d\n", i, clus1 ); </span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "hairetsu ga kowareta (in treebase, after conjuction) !\n" ); </span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; j<clus2; j++ )</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( mseq2[j] ) != len2 ) </span></span>
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231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="232" 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">
232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "j = %d / %d\n", j, clus2 ); </span></span>
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233
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "hairetsu ga kowareta (in treebase, after conjuction) !\n" ); </span></span>
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<td class="old_line diff-line-num old" data-linenumber="234" 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">
234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"></span>
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239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"></span>
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240
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<pre style="margin: 0;">-<span id="LC240" 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="LC241" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) </span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="243" 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">
243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( mseq1[i] ) != len1 ) </span></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="245" 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">
245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "i = %d / %d\n", i, clus1 ); </span></span>
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<td class="old_line diff-line-num old" data-linenumber="246" 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">
246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "hairetsu ga kowareta (in treebase, after free topol) !\n" ); </span></span>
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<td class="old_line diff-line-num old" data-linenumber="247" 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">
247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; j<clus2; j++ )</span></span>
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<td class="old_line diff-line-num old" data-linenumber="251" 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">
251
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC251" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="252" 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">
252
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC252" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( mseq2[j] ) != len2 ) </span></span>
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<td class="old_line diff-line-num old" data-linenumber="253" 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">
253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="254" 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">
254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "j = %d / %d\n", j, clus2 ); </span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "hairetsu ga kowareta (in treebase, after free topol) !\n" ); </span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="262" 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">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( trap_g, "\nSTEP-%d\n", l );</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( trap_g, "group1 = %s\n", indication1 );</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( trap_g, "group2 = %s\n", indication2 );</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="266" 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">
266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\rSTEP % 5d / %d %d-%d", l+1, njob-1, clus1, clus2 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="267" 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">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">STEP % 5d / %d "</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="268" 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">
268
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC268" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">callback</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">callback</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="s" style="color: #d14;">"Progressive alignment"</span> <span class="p">)</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">chudan_tbfast</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="269" 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">
269
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC269" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="270" 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">
270
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC270" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\nclus1=%d, clus2=%d\n", clus1, clus2 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="271" 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">
271
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC271" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="273" 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">
273
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC273" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="274" 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">
274
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC274" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "STEP %d /%d\n", l+1, njob-1 );</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "group1 = %.66s", indication1 );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="276" 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">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( indication1 ) > 66 ) reporterr( "..." );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="277" 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">
277
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC277" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="278" 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">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "group2 = %.66s", indication2 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="279" 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">
279
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC279" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( strlen( indication2 ) > 66 ) reporterr( "..." );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="280" 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">
280
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC280" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="281" 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">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="old_line diff-line-num old" data-linenumber="282" 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">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="283" 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">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="old_line diff-line-num old" data-linenumber="284" 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">
284
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC284" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "before align all\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="285" 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">
285
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC285" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> display( aseq, njob );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="286" 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">
286
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC286" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="287" 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">
287
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC287" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "before align 1 %s \n", indication1 );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="288" 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">
288
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC288" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> display( mseq1, clus1 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="289" 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">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="290" 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">
290
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC290" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "before align 2 %s \n", indication2 );</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="291" 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">
291
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC291" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> display( mseq2, clus2 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="292" 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">
292
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC292" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="293" 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">
293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="295" 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">
295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="296" 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">
296
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC296" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nevermemsave</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="n" style="color: #333;">len1</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">30000</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">len2</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">30000</span> <span class="p">)</span> <span class="p">)</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="297" 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">
297
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC297" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="298" 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">
298
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC298" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">len1=%d, len2=%d, Switching to the memsave mode</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;">len1</span><span class="p">,</span> <span class="n" style="color: #333;">len2</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="299" 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">
299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">commonIP</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">commonIP</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">commonIP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">commonAlloc1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">commonAlloc2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="p">)</span> <span class="n" style="color: #333;">ffttry</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ffttry</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="LC309" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000); // v6.708</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (double)len1/fftlog[m1], clus1, (double)len2/fftlog[m2], clus2 );</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">force_fft</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span> <span class="n" style="color: #333;">use_fft</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ffttry</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" f</span><span class="se" style="color: #d14;">\b\b</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span> <span class="p">)</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"m"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Falign_udpari_long</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</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;">fftlog</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">m1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Falign</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</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;">fftlog</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "######### mseq1[0] = %s\n", mseq1[0] );</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" d</span><span class="se" style="color: #d14;">\b\b</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m1</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>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span> <span class="n" style="color: #333;">alg</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'a'</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Aalign</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'M'</span> <span class="p">):</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</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;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"m"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MSalignmm</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'d'</span> <span class="p">):</span></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus2</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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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"> <span class="p">{</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G__align11</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span 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;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span> <span class="p">);</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"> <span class="p">}</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="c"> <span class="p">{</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D__align_ls</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dumdb</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="c"> <span class="p">}</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span> <span class="sc" style="color: #d14;">'A'</span> <span class="p">):</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus2</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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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d-%d", clus1, clus2 );</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G__align11</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span 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;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span> <span class="p">);</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"> <span class="p">}</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"> <span class="p">{</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">500</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="p">)</span> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">" h"</span> <span class="p">);</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\n\n %d - %d (%d x %d) : \n", topol[l][0][0], topol[l][1][0], clus1, clus2 );</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">pscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span><span class="p">,</span> <span class="n" style="color: #333;">penalty</span><span class="p">,</span> <span class="n" style="color: #333;">penalty_ex</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">effarr1</span><span class="p">,</span> <span class="n" style="color: #333;">effarr2</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dumdb</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">outgap</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild0</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxchild1</span><span class="p">,</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"> <span class="nl">default:</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"> <span class="n" style="color: #333;">ErrorExit</span><span class="p">(</span> <span class="s" style="color: #d14;">"ERROR IN SOURCE FILE"</span> <span class="p">);</span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"> <span class="p">}</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> <span class="p">}</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SCOREOUT</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"score = %10.2f</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;">pscore</span> <span class="p">);</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"> <span class="n" style="color: #333;">tscore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pscore</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m1</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;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="p">);</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// writePre( njob, name, nlen, aseq, 0 );</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">disp</span> <span class="p">)</span> <span class="n" style="color: #333;">display</span><span class="p">(</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\n" );</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="382" 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">
382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// jissainiha nai. atarashii hairetsu ha saigo dakara.</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"> <span class="p">{</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"Check source!!!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="385" 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">
385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="c"> <span class="p">}</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">mergeoralign</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span> <span class="p">)</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"> <span class="p">{</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( localkeeplength ) ndeleted += deletenewinsertions( clus1, clus2, mseq1, mseq2, NULL );</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<clus1; i++ ) reporterr( ">STEP0 mseq1[%d] = \n%s\n", i, mseq1[i] );</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<clus2; i++ ) reporterr( ">STEP0 mseq2[%d] = \n%s\n", i, mseq2[i] );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="392" 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">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="c"> <span class="n" style="color: #333;">gapmaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">len1nocommongap</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">len1</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"> <span class="n" style="color: #333;">adjustgapmap</span><span class="p">(</span> <span class="n" style="color: #333;">gapmaplen</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="396" 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">
396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) reporterr( ">STEP1 mseq1[%d] = \n%s\n", i, mseq1[i] );</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus2; i++ ) reporterr( ">STEP1 mseq2[%d] = \n%s\n", i, mseq2[i] );</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( clus1 + clus2 < njob ) restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen, '-' );</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">smoothing</span> <span class="p">)</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"> <span class="p">{</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="n" style="color: #333;">restorecommongapssmoothly</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">clus1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clus2</span><span class="p">),</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span> <span class="p">);</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">findnewgaps</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">gaplen</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="404" 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">
404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="c"> <span class="n" style="color: #333;">insertnewgaps_bothorders</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">alreadyaligned</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gaplen</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</span> <span class="n" style="color: #333;">gapmaplen</span><span class="p">,</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;">alg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span> <span class="p">);</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="p">}</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="408" 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">
408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="n" style="color: #333;">restorecommongaps</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">clus1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clus2</span><span class="p">),</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alloclen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="409" 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">
409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">findnewgaps</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">gaplen</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="410" 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">
410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"> <span class="n" style="color: #333;">insertnewgaps</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">alreadyaligned</span><span class="p">,</span> <span class="n" style="color: #333;">aseq</span><span class="p">,</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gaplen</span><span class="p">,</span> <span class="n" style="color: #333;">gapmap</span><span class="p">,</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;">alg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="411" 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">
411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"> <span class="p">}</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="413" 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">
413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="414" 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">
414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="415" 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">
415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) reporterr( ">STEP3 mseq1[%d] = \n%s\n", i, mseq1[i] );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="416" 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">
416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus2; i++ ) reporterr( ">STEP3 mseq2[%d] = \n%s\n", i, mseq2[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC419" 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="LC420" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<njob; i++ ) eq2dash( aseq[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) </span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mseq1[%d] bef change = %s\n", i, mseq1[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> eq2dash( mseq1[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mseq1[%d] aft change = %s\n", i, mseq1[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus2; i++ ) </span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mseq2[%d] bef change = %s\n", i, mseq2[i] );</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> eq2dash( mseq2[i] );</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mseq2[%d] aft change = %s\n", i, mseq2[i] );</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) eq2dash( mseq1[i] );</span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus2; i++ ) eq2dash( mseq2[i] );</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">eq2dashmatometehayaku</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">,</span> <span class="n" style="color: #333;">clus1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="c"> <span class="n" style="color: #333;">eq2dashmatometehayaku</span><span class="p">(</span> <span class="n" style="color: #333;">mseq2</span><span class="p">,</span> <span class="n" style="color: #333;">clus2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC441" 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="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="mi" style="color: #099;">1</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 class="n" style="color: #333;">alreadyaligned</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">newdistmtx</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// tsukawanai</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC446" 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="LC447" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "group1 = " );</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<clus1; i++ ) reporterr( "%d ", topol[l][0][i] );</span></span>
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<pre style="margin: 0;">-<span id="LC449" 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="LC450" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "group2 = " );</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( m=0; m<clus2; m++ ) reporterr( "%d ", topol[l][1][m] );</span></span>
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<pre style="margin: 0;">-<span id="LC452" 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="LC453" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="c"> <span class="n" style="color: #333;">skiptable1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</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="LC456" class="line" lang="c"> <span class="n" style="color: #333;">skiptable2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">clus2</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="LC457" class="line" lang="c"> <span class="n" style="color: #333;">makeskiptable</span><span class="p">(</span> <span class="n" style="color: #333;">clus1</span><span class="p">,</span> <span class="n" style="color: #333;">skiptable1</span><span class="p">,</span> <span class="n" style="color: #333;">mseq1</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// allocate suru.</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="c"> <span class="n" style="color: #333;">makeskiptable</span><span class="p">(</span> <span class="n" style="color: #333;">clus2</span><span class="p">,</span> <span class="n" style="color: #333;">skiptable2</span><span class="p">,</span> <span class="n" style="color: #333;">mseq2</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// allocate suru.</span></span>
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<pre style="margin: 0;">-<span id="LC459" 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="LC460" 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;">clus1</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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<pre style="margin: 0;">-<span id="LC461" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// makeskiptable( 1, skiptable1, mseq1+i ); // allocate suru.</span></span>
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<pre style="margin: 0;">-<span id="LC464" 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="LC465" class="line" lang="c"> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="c"> <span class="n" style="color: #333;">ssi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">clus2</span><span class="p">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="c"> <span class="n" style="color: #333;">ssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selfscore</span><span class="p">[</span><span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">m</span><span class="p">]];</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="c"> <span class="n" style="color: #333;">tm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">m</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tm</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="c"> <span class="n" style="color: #333;">immin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">immax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tm</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">immin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tm</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">immax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;">bunbo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span> <span class="n" style="color: #333;">ssi</span><span class="p">,</span> <span class="n" style="color: #333;">ssm</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">bunbo</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="LC483" class="line" lang="c"> <span class="n" style="color: #333;">newdistmtx</span><span class="p">[</span><span class="n" style="color: #333;">immin</span><span class="p">][</span><span class="n" style="color: #333;">immax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">immin</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 2013/Oct/17</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="c"> <span class="n" style="color: #333;">newdistmtx</span><span class="p">[</span><span class="n" style="color: #333;">immin</span><span class="p">][</span><span class="n" style="color: #333;">immax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">immin</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">naivepairscorefast</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mseq2</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">],</span> <span class="n" style="color: #333;">skiptable1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">skiptable2</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">],</span> <span class="n" style="color: #333;">penalty_dist</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bunbo</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">newdistmtx</span><span class="p">[</span><span class="n" style="color: #333;">immin</span><span class="p">][</span><span class="n" style="color: #333;">immax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">immin</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">naivepairscore11</span><span class="p">(</span> <span class="n" style="color: #333;">mseq1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mseq2</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">],</span> <span class="n" style="color: #333;">penalty_dist</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bunbo</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" 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="LC490" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="c"> <span class="p">}</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable1</span> <span class="p">);</span> <span class="n" style="color: #333;">skiptable1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable2</span> <span class="p">);</span> <span class="n" style="color: #333;">skiptable2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" 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="LC496" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="c"></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l][0] ); topol[l][0] = NULL;</span></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l][1] ); topol[l][1] = NULL;</span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// free( topol[l] ); topol[l] = NULL;</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="c"></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( ">514\n%s\n", aseq[514] );</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">);</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="c"> <span class="p">}</span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="c"></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SCOREOUT</span></span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"totalscore = %10.2f</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tscore</span> <span class="p">);</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">Falign</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="512" 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">
512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">Falign_udpari_long</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="513" 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">
513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="514" 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">
514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">D__align</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="515" 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">
515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">G__align11</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// iru?</span></span>
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<td class="old_line diff-line-num old" data-linenumber="516" 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">
516
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC516" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">effarr1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="517" 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">
517
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC517" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">effarr2</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="518" 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">
518
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC518" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">indication1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="519" 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">
519
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC519" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">indication2</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="520" 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">
520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="521" 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">
521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gaplen</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="522" 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">
522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapmap</span> <span class="p">);</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</span> <span class="p">)</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</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="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">alreadyaligned</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;">free</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span> <span class="p">);</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">effarr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="c"></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="c"> <span class="nl">chudan_tbfast:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="531" 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">
531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="532" 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">
532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="c"> <span class="n" style="color: #333;">Falign</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="533" 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">
533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">Falign_udpari_long</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="534" 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">
534
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC534" class="line" lang="c"> <span class="n" style="color: #333;">A__align</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="535" 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">
535
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC535" class="line" lang="c"> <span class="n" style="color: #333;">D__align</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="536" 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">
536
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC536" class="line" lang="c"> <span class="n" style="color: #333;">G__align11</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// iru?</span></span>
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<td class="old_line diff-line-num old" data-linenumber="537" 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">
537
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC537" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">effarr1</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">effarr1</span> <span class="p">);</span> <span class="n" style="color: #333;">effarr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="538" 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">
538
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC538" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">effarr2</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">effarr2</span> <span class="p">);</span> <span class="n" style="color: #333;">effarr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">indication1</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">indication1</span> <span class="p">);</span> <span class="n" style="color: #333;">indication1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">indication2</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">indication2</span> <span class="p">);</span> <span class="n" style="color: #333;">indication2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span> <span class="p">);</span> <span class="n" style="color: #333;">fftlog</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplen</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gaplen</span> <span class="p">);</span> <span class="n" style="color: #333;">gaplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapmap</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">gapmap</span> <span class="p">);</span> <span class="n" style="color: #333;">gapmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alreadyaligned</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">alreadyaligned</span> <span class="p">);</span> <span class="n" style="color: #333;">alreadyaligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">specificityconsideration</span> <span class="p">)</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="c"> <span class="p">{</span></span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">dynamicmtx</span> <span class="p">);</span> <span class="n" style="color: #333;">dynamicmtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span> <span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">localmem</span> <span class="p">);</span> <span class="n" style="color: #333;">localmem</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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550
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SKIP</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable1</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable1</span> <span class="p">);</span> <span class="n" style="color: #333;">skiptable1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable2</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeIntMtx</span><span class="p">(</span> <span class="n" style="color: #333;">skiptable2</span> <span class="p">);</span> <span class="n" style="color: #333;">skiptable2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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553
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<pre style="margin: 0;">-<span id="LC553" 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="LC554" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#d787ec50dfd9048f1124ca832aadca4ce7a4b51a"><strong>core/tbfast.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">@@ -1248,7 +1248,8 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq</td>
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1248
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1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfiles</span><span class="p">;</span></span>
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1249
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<pre style="margin: 0;"> <span id="LC1249" 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;">cpmxhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1250" 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;">memhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1251
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<pre style="margin: 0;">-<span id="LC1251" 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;">cpmxchild0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cpmxchild1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1251" 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;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1252" 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;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1252
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1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">orieff1</span><span class="p">,</span> <span class="n" style="color: #333;">orieff2</span><span class="p">;</span></span>
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1253
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1254
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if REPORTCOSTS</span></span>
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">time_t</span> <span class="n" style="color: #333;">starttime</span><span class="p">,</span> <span class="n" style="color: #333;">startclock</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1365" 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">@@ -1365,8 +1366,8 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq</td>
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1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1367
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="c"> <span class="p">{</span></span>
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "l=%d, dep[l].child0=%d, dep[l].child1=%d\n", l, dep[l].child0, dep[l].child1 );</span></span>
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1368
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<pre style="margin: 0;">-<span id="LC1368" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p"><span class="idiff right">]</span>;</span></span>
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1369
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<pre style="margin: 0;">-<span id="LC1369" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</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="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</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="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cpmxchild1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpmxhist</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">dep</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="n" style="color: #333;">child1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "cpmxchild0=%p, cpmxchild1=%p\n", cpmxchild0, cpmxchild1 );</span></span>
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1373" 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">@@ -1717,12 +1718,27 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq</td>
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1717
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1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="c"> <span class="n" style="color: #333;">reporterr</span><span class="p">(</span> <span class="s" style="color: #d14;">"user = %f min</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)(</span><span class="n" style="color: #333;">clock</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">startclock</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">CLOCKS_PER_SEC</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">60</span><span class="p">);</span></span>
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1718
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1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1719
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1720
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<pre style="margin: 0;"> <span id="LC1720" class="line" lang="c"></span>
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1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1 // 2021/Jun/25</span></span>
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1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">)</span> </span>
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1723
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<pre style="margin: 0;">+<span id="LC1723" class="line" lang="c"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1724
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<pre style="margin: 0;">+<span id="LC1724" 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;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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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1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="c"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">)</span> </span>
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1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="c"> <span class="p">{</span></span>
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1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxhist[%d]\n", i );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="c"> <span class="p">}</span></span>
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1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="c"> <span class="p">}</span></span>
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1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="c"> <span class="p">}</span></span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1720
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1735
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<pre style="margin: 0;"> <span id="LC1735" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">)</span> </span>
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1721
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1736
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<pre style="margin: 0;"> <span id="LC1736" class="line" lang="c"> <span class="p">{</span></span>
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1722
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1737
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<pre style="margin: 0;"> <span id="LC1737" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "freeing cpmxhist[njob-2]\n" );</span></span>
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1723
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1738
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<pre style="margin: 0;"> <span id="LC1738" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span><span class="p">[</span><span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1724
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<td class="new_line diff-line-num" data-linenumber="1739" 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">
1739
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<pre style="margin: 0;"> <span id="LC1739" class="line" lang="c"> <span class="p">}</span></span>
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1725
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<td class="new_line diff-line-num" data-linenumber="1740" 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">
1740
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<pre style="margin: 0;"> <span id="LC1740" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="p">);</span> <span class="n" style="color: #333;">cpmxhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1726
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<td class="new_line diff-line-num" data-linenumber="1742" 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">
1742
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">memhist</span> <span class="p">);</span> <span class="n" style="color: #333;">memhist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1727" 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">
1727
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1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="c"></span>
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1728
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if SCOREOUT</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1868" 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="1884" 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">@@ -1868,8 +1884,9 @@ int main( int argc, char *argv[] )</td>
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1868
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<td class="new_line diff-line-num" data-linenumber="1884" 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">
1884
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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">iscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">iscore_kozo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1869" 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">
1869
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<td class="new_line diff-line-num" data-linenumber="1885" 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">
1885
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<pre style="margin: 0;"> <span id="LC1885" 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;">skiptable</span><span class="p">;</span></span>
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1870
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<td class="new_line diff-line-num" data-linenumber="1886" 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">
1886
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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff_kozo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eff_kozo_mapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1871
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<td class="new_line diff-line-num old" data-linenumber="1887" 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="LC1871" 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;">ien</span><span class="p">,</span> <span class="n" style="color: #333;">ik</span><span class="p">,</span> <span class="n" style="color: #333;">jk</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1887
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<pre style="margin: 0;">+<span id="LC1887" 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;"><span class="idiff left">k</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ien</span><span class="p">,</span> <span class="n" style="color: #333;">ik</span><span class="p">,</span> <span class="n" style="color: #333;">jk</span><span class="p">;</span></span>
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1872
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<td class="new_line diff-line-num" data-linenumber="1888" 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">
1888
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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">topol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">topol_kozo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1889
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<pre style="margin: 0;">+<span id="LC1889" 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;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1873
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<td class="new_line diff-line-num" data-linenumber="1890" 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">
1890
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<pre style="margin: 0;"> <span id="LC1890" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">addmem</span><span class="p">;</span></span>
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1874
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<td class="new_line diff-line-num" data-linenumber="1891" 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">
1891
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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Treedep</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1875" 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">
1875
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<td class="new_line diff-line-num" data-linenumber="1892" 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">
1892
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<pre style="margin: 0;"> <span id="LC1892" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">len_kozo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2041" 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="2058" 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">@@ -2041,6 +2058,45 @@ int main( int argc, char *argv[] )</td>
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2041
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<td class="new_line diff-line-num" data-linenumber="2058" 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">
2058
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<pre style="margin: 0;"> <span id="LC2058" class="line" lang="c"> <span class="n" style="color: #333;">readData_pointer</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span> <span class="p">);</span></span>
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2042
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2059
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<pre style="margin: 0;"> <span id="LC2059" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span> <span class="p">);</span></span>
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2043
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2060
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<pre style="margin: 0;"> <span id="LC2060" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2061
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<pre style="margin: 0;">+<span id="LC2061" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">treein</span> <span class="p">)</span></span>
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2062
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<pre style="margin: 0;">+<span id="LC2062" class="line" lang="c"> <span class="p">{</span></span>
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2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1 // pairlocalalign() yori mae ni hitsuyou, specificityconsideration>0.0 && usertree no toki.</span></span>
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2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="c"> <span class="n" style="color: #333;">loadtree</span><span class="p">(</span> <span class="n" style="color: #333;">njob</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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">dep</span><span class="p">,</span> <span class="n" style="color: #333;">treeout</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// loadtop( njob, topol, len, name, NULL, dep ); // 2015/Jan/13, not yet checked</span></span>
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2066
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<pre style="margin: 0;">+<span id="LC2066" 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;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">done.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<njob-1; i++ ) reporterr( "%d-%d, %f-%f\n", topol[i][0][0], topol[i][1][0], len[i][0], len[i][1] );</span></span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">callpairlocalalign</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">specificityconsideration</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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2069
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<pre style="margin: 0;">+<span id="LC2069" class="line" lang="c"> <span class="p">{</span></span>
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2070
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<pre style="margin: 0;">+<span id="LC2070" 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;">mem0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">),</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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2071
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<pre style="margin: 0;">+<span id="LC2071" 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;">mem1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">),</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="c"> <span class="n" style="color: #333;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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2073
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<pre style="margin: 0;">+<span id="LC2073" 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;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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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2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="c"> <span class="p">{</span></span>
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2075
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<pre style="margin: 0;">+<span id="LC2075" class="line" lang="c"> <span class="n" style="color: #333;">topolorderz</span><span class="p">(</span> <span class="n" style="color: #333;">mem0</span><span class="p">,</span> <span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="n" style="color: #333;">dep</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="c"> <span class="n" style="color: #333;">topolorderz</span><span class="p">(</span> <span class="n" style="color: #333;">mem1</span><span class="p">,</span> <span class="n" style="color: #333;">topol</span><span class="p">,</span> <span class="n" style="color: #333;">dep</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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2077
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<pre style="margin: 0;">+<span id="LC2077" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mem0=\n" );</span></span>
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2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; mem0[j]!=-1; j++ ) reporterr( "%d ", mem0[j] );</span></span>
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "mem1=\n" );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( j=0; mem1[j]!=-1; j++ ) reporterr( "%d ", mem1[j] );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2083
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<pre style="margin: 0;">+<span id="LC2083" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "\n" );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2085
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<pre style="margin: 0;">+<span id="LC2085" 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;">mem0</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">k</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;">mem1</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2086
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<pre style="margin: 0;">+<span id="LC2086" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2087
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="c"> <span class="n" style="color: #333;">expdist</span><span class="p">[</span><span class="n" style="color: #333;">mem0</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]][</span><span class="n" style="color: #333;">mem1</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span> <span class="n" style="color: #333;">len</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2088
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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="c"> <span class="n" style="color: #333;">expdist</span><span class="p">[</span><span class="n" style="color: #333;">mem1</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]][</span><span class="n" style="color: #333;">mem0</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span> <span class="n" style="color: #333;">len</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ )</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> reporterr( "expdist[%d][%d] = %f\n", i, j, expdist[i][j] );</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mem0</span> <span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">mem1</span> <span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="c"> <span class="p">}</span></span>
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2044
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2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="c"></span>
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2045
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2101
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<pre style="margin: 0;"> <span id="LC2101" 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="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 class="c1" style="color: #998; font-style: italic;">// compacttree == 3 no toki ha hat3dir/uselh no joho wo tsukau, 2016/Jan</span></span>
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2046
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2102
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<pre style="margin: 0;"> <span id="LC2102" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2107" 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="2163" 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">@@ -2107,9 +2163,10 @@ int main( int argc, char *argv[] )</td>
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2107
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2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "pav[0]=%s\n", pav[0] );</span></span>
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2108
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2164
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<pre style="margin: 0;"> <span id="LC2164" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">callpairlocalalign</span> <span class="p">)</span></span>
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2109
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2165
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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="c"> <span class="p">{</span></span>
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2110
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<pre style="margin: 0;">-<span id="LC2110" class="line" lang="c"> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nlenmax</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iscore</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">pac</span><span class="p">,</span> <span class="n" style="color: #333;">pav</span> <span class="p">);</span></span>
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2166
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<pre style="margin: 0;">+<span id="LC2166" class="line" lang="c"> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nlenmax</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iscore</span><span class="p">,</span> <span class="n" style="color: #333;">localhomtable</span><span class="p">,</span> <span class="n" style="color: #333;">pac</span><span class="p">,</span> <span class="n" style="color: #333;">pav</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expdist</span></span> <span class="p">);</span></span>
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2111
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2167
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<pre style="margin: 0;"> <span id="LC2167" class="line" lang="c"> <span class="n" style="color: #333;">arguments</span><span class="p">(</span> <span class="n" style="color: #333;">tac</span><span class="p">,</span> <span class="n" style="color: #333;">tav</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// anzen no tame</span></span>
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2112
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2168
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<pre style="margin: 0;"> <span id="LC2168" class="line" lang="c"> <span class="n" style="color: #333;">callpairlocalalign</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// wakarinikui.</span></span>
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2169
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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">);</span> <span class="n" style="color: #333;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2113
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2170
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<pre style="margin: 0;"> <span id="LC2170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fastathreshold</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">0001</span> <span class="p">)</span> <span class="n" style="color: #333;">constraint</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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2114
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2171
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<pre style="margin: 0;"> <span id="LC2171" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "blosum %d / kimura 200\n", nblosum );</span></span>
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2115
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2172
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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "scoremtx=%d\n", scoremtx );</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2261" 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">@@ -2261,9 +2318,10 @@ int main( int argc, char *argv[] )</td>
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2261
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2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="c"> <span class="p">{</span></span>
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2262
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2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">callpairlocalalign</span> <span class="p">)</span></span>
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2263
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2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="c"> <span class="p">{</span></span>
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2264
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<pre style="margin: 0;">-<span id="LC2264" class="line" lang="c"> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nlenmax</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iscore</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">pac</span><span class="p">,</span> <span class="n" style="color: #333;">pav</span> <span class="p">);</span></span>
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2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="c"> <span class="n" style="color: #333;">pairlocalalign</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nlenmax</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iscore</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">pac</span><span class="p">,</span> <span class="n" style="color: #333;">pav</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expdist</span></span> <span class="p">);</span></span>
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2265
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2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="c"> <span class="n" style="color: #333;">arguments</span><span class="p">(</span> <span class="n" style="color: #333;">tac</span><span class="p">,</span> <span class="n" style="color: #333;">tav</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// anzen no tame</span></span>
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2266
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2323
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<pre style="margin: 0;"> <span id="LC2323" class="line" lang="c"> <span class="n" style="color: #333;">callpairlocalalign</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// wakarinikui.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2324
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<pre style="margin: 0;">+<span id="LC2324" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">expdist</span> <span class="p">);</span> <span class="n" style="color: #333;">expdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2267
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<td class="new_line diff-line-num" data-linenumber="2325" 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">
2325
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<pre style="margin: 0;"> <span id="LC2325" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fastathreshold</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">0001</span> <span class="p">)</span> <span class="n" style="color: #333;">constraint</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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2268
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2326
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<pre style="margin: 0;"> <span id="LC2326" 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;">"blosum %d / kimura 200</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;">nblosum</span> <span class="p">);</span></span>
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2269
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<td class="new_line diff-line-num" data-linenumber="2327" 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">
2327
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<pre style="margin: 0;"> <span id="LC2327" 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;">"scoremtx=%d</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;">scoremtx</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2448" 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="2506" 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">@@ -2448,16 +2506,13 @@ int main( int argc, char *argv[] )</td>
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2448
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2506
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<pre style="margin: 0;"> <span id="LC2506" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="2449" 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">
2449
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<td class="new_line diff-line-num" data-linenumber="2507" 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">
2507
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<pre style="margin: 0;"> <span id="LC2507" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">treein</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2450" 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">
2450
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<td class="new_line diff-line-num" data-linenumber="2508" 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">
2508
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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2451" 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">
2451
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2451" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2452" 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">
2452
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2452" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( nkozo )</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2453" 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">
2453
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2453" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2454" 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">
2454
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2454" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fprintf( stderr, "Both structure and user tree have been given. Not yet supported!\n" );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2455" 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">
2455
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2455" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2456" 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">
2456
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2456" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2457
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<td class="new_line diff-line-num old" data-linenumber="2509" 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="LC2457" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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2509
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<pre style="margin: 0;">+<span id="LC2509" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 // pairlocalalign() yori mae ni idou, 2021/Jun.</span></span>
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2458
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2510
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<pre style="margin: 0;"> <span id="LC2510" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> loadtree( njob, topol, len, name, nlen, dep, treeout );</span></span>
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<td class="old_line diff-line-num" data-linenumber="2459" 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">
2459
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<td class="new_line diff-line-num" data-linenumber="2511" 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">
2511
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<pre style="margin: 0;"> <span id="LC2511" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">// loadtop( njob, topol, len, name, NULL, dep ); // 2015/Jan/13, not yet checked</span></span>
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2460
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<td class="new_line diff-line-num" data-linenumber="2512" 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">
2512
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<pre style="margin: 0;"> <span id="LC2512" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fprintf( stderr, "\ndone.\n\n" );</span></span>
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2513
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<pre style="margin: 0;">+<span id="LC2513" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<njob-1; i++ ) reporterr( "%d-%d, %f-%f\n", topol[i][0][0], topol[i][1][0], len[i][0], len[i][1] );</span></span>
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2514
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<pre style="margin: 0;">+<span id="LC2514" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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2515
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<pre style="margin: 0;">+<span id="LC2515" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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2461
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2516
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<pre style="margin: 0;"> <span id="LC2516" class="line" lang="c"> <span class="p">}</span></span>
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2462
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2517
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<pre style="margin: 0;"> <span id="LC2517" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2463
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2518
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<pre style="margin: 0;"> <span id="LC2518" class="line" lang="c"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#5584b7e2129a1bb4aa5dabe72bb6a85d2efa2d9f"><strong>core/univscript.tmpl</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">@@ -5,15 +5,17 @@ for prog in $progs; do</td>
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5
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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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6
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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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7
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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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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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">make CC="/opt/homebrew-x86_64/bin/gcc-11" CFLAGS="-O3 -arch x86_64 -mmacosx-version-min=10.9 -DMACOSX_DEPLOYMENT_TARGET=10.9" LIBS="-static-libgcc -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">rm -f dash_client</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">env CC='/opt/homebrew-x86_64/bin/gcc-11 -static-libgcc -O3 -arch x86_64' GOARCH=amd64 GOOS=darwin CGO_ENABLED=0 /opt/homebrew-x86_64/bin/go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">for prog in $progs; do</span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> mv $prog $prog.x86_64</span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">done</span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">make clean</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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">make CC="/opt/homebrew/bin/gcc-11" CFLAGS="-static-libgcc -O3 -arch arm64 -mmacosx-version-min=11.1 -DMACOSX_DEPLOYMENT_TARGET=11.1" LIBS="-lm -lpthread" ENABLE_MULTITHREAD="-Denablemultithread"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">rm -f dash_client</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">env CC='/opt/homebrew/bin/gcc-11 -static-libgcc -O3 -arch arm64' GOARCH=arm64 GOOS=darwin CGO_ENABLED=0 /opt/homebrew/bin/go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">for prog in $progs; do</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> mv $prog $prog.arm64</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">done</span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/084720ae6bcfcbd90efef804bf7aa7bb16731de4#f78a71af8bbf8cc2f6f313549d4da14bd3771359"><strong>readme</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> MAFFT: a multiple sequence alignment program</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.48<span class="idiff left">1</span>, 2021/<span class="idiff right">May/26</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.48<span class="idiff left">6</span>, 2021/<span class="idiff right">Jul/19</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> http://mafft.cbrc.jp/alignment/software/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> katoh@ifrec.osaka-u.ac.jp</span>
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