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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/214cac8d75173432c71c2ec177d2b93e542bd07e">214cac8d</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-12-31T17:03:58+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1170</pre>
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<h4>5 changed files:</h4>
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<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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<li class="file-stats">
<a href="#5f9dbaf068df9da9d036ea6546a588a0c71778be">
src/LastEvaluer.cc
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<li class="file-stats">
<a href="#b8658dba55bc28b741dfef5e4ea001b2623bdb9e">
src/mcf_frameshift_xdrop_aligner.cc
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<a href="#7b7b86f617ae717ef44a71c27b54fe7b613973d1">
src/mcf_frameshift_xdrop_aligner.hh
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/214cac8d75173432c71c2ec177d2b93e542bd07e#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-12-28 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * src/LastEvaluer.cc, src/mcf_frameshift_xdrop_aligner.cc,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> src/mcf_frameshift_xdrop_aligner.hh, test/last-test.out:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Fix E-values for new-style frameshifts</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [a55b81199602] [tip]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">2020-12-23 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * scripts/last-train, src/LastEvaluer.cc:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Try to fix floating-point infinite loops</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> [829c63f50494]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [829c63f50494]</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">2020-12-15 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="5f9dbaf068df9da9d036ea6546a588a0c71778be">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/214cac8d75173432c71c2ec177d2b93e542bd07e#5f9dbaf068df9da9d036ea6546a588a0c71778be"><strong>src/LastEvaluer.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="427" style="width: 35px; color: rgba(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="427" style="width: 35px; color: rgba(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">@@ -427,6 +427,7 @@ void LastEvaluer::initFrameshift(const const_dbl_ptr *substitutionProbs,</td>
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="n" style="color: #333;">aligner</span><span class="p">;</span></span>
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">200</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx long enough to avoid edge effects ???</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tranDnaLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">origDnaLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tranDnaLength</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="LC431" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// suggested by Y-K Yu, R Bundschuh, T Hwa, 2002</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</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;">numOfAlignments</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="LC433" class="line" lang="cpp"></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">@@ -446,18 +447,18 @@ void LastEvaluer::initFrameshift(const const_dbl_ptr *substitutionProbs,</td>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="n" style="color: #333;">protein</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;">pDist</span><span class="p">(</span><span class="n" style="color: #333;">randGen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tranDnaLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="n" style="color: #333;">tranDna</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;">tDist</span><span class="p">(</span><span class="n" style="color: #333;">randGen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">maxSumOfProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">protein</span><span class="p">,</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">tranDna</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">tranDna</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">probRatioSum</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;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"simScore: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</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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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max likelihood k = 1 / (m * n * avg[exp(-lambda * score)])</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probRatioSum</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probRatioSum</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"lambda k m n: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaLength</span> <span class="o" style="font-weight: 600;"><<</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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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaLength</span> <span class="o" style="font-weight: 600;"><<</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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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEvaluerParameters</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">k</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="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="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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<a href="https://salsa.debian.org/med-team/last-align/-/commit/214cac8d75173432c71c2ec177d2b93e542bd07e#b8658dba55bc28b741dfef5e4ea001b2623bdb9e"><strong>src/mcf_frameshift_xdrop_aligner.cc</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">@@ -381,7 +381,7 @@ void FrameshiftXdropAligner::count(bool isRightwardExtension,</td>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">FrameshiftXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maxSumOfProbRatios</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">protein</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDna</span><span class="p">,</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" style="width: 35px; color: rgba(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">@@ -394,45 +394,27 @@ double FrameshiftXdropAligner::maxSumOfProbRatios(const uchar *protein,</td>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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395
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"></span>
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396
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinLength</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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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">tranDnaSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tran</span>DnaLength</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="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tranDnaSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proteinSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tran</span>DnaSize</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">origDnaSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orig</span>DnaLength</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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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">origDnaSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proteinSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orig</span>DnaSize</span><span class="p">);</span></span>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <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;">delRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="cpp"> <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;">newRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaSize</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <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;">newRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaSize</span><span class="p">;</span></span>
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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="n" style="color: #333;">Z1</span><span class="p">,</span> <span class="n" style="color: #333;">Z2</span><span class="p">,</span> <span class="n" style="color: #333;">Z3</span><span class="p">;</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxValue</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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402
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb1</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</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="cpp"> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</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;">proteinSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</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="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</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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<pre style="margin: 0;">-<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill_n</span><span class="p">(</span><span class="n" style="color: #333;">delRow</span><span class="p">,</span> <span class="n" style="color: #333;">origDnaSize</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</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="LC424" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y3</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="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">proteinSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</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="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">=</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>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</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 class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">origDnaSize</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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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430
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tran</span>DnaSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</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="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orig</span>DnaSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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432
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span><span class="p">;</span></span>
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433
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span><span class="p">;</span></span>
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434
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldRow</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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</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;">1</span><span class="p">]];</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isMain</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">oldRow</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;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</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;">3</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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436
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>
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437
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb2</span><span class="p">;</span></span>
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438
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="446" style="width: 35px; color: rgba(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">@@ -446,45 +428,24 @@ double FrameshiftXdropAligner::maxSumOfProbRatios(const uchar *protein,</td>
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446
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">origDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxValue</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">fill_n</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">delRow</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">origDnaSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</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>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">maxValue</span><span class="p">,</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">newRow</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="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</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="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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="LC472" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y3</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="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">maxValue</span><span class="p">,</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">newRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinSize</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">origDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">=</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;">proteinLength</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</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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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">origDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</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="LC442" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">tranDnaLength</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</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>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">origDnaSize</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</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>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</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="LC487" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldRow</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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</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="LC447" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">isIn</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">origDnaLength</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="LC448" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isMain</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">oldRow</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;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</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;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</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">@@ -55,8 +55,9 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tranDna should point to translated DNA: frame 012012012...</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// origDnaLength is the length of the untranslated DNA sequence</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxSumOfProbRatios</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">protein</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDna</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">tran</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDna</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">orig</span>DnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"11<span class="idiff left right">69</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"11<span class="idiff left right">70</span>"</span></span></pre>
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